As a long-time DM relatively new to D&D/Pathfinder, I've recently become aware of spells that many consider to be "breakers" (my term) :
Battle breaker - significantly turns the tide in battle, with little that can be done about it
Mystery breaker - short-circuits looking for clues, figuring things out, using skill rolls, etc.
Death breaker - allows PC's to not worry about death or negative levels
Story breaker - most of the time, short-circuits the need for
traveling from point A to point B (which takes time, provides opportunities for encounters and side-adventures, etc.)
Counterspell breaker - there's only maybe 1-3 spells that can effectively counter or get around the spell
I'm most interested in spells of 4th level and higher. Below is a partial list I've cobbled together from various forums.
Please feel free to add your own pet peeves, or argue against any of the spells in this list. It's not "my" list, I don't care. 
Please do
not feel obligated to fit your spell into one of my categories, just say what you don't like about it.
But please do be kind enough to indicate the spell level of any spell you name. Thanks!
Charm Person/Monster (1/4) - story breaker. I don't like "person" spells to begin with. The spell is unclear and you can cast it too quickly. Being able to make an instant friend in combat causes nothing but groaning at the table, and the duration is also too long for how quickly you can cast it. I would like to reference 4e for a fix, but that's only a partway fix. 4e has at least three ways of replicating the spell, none in the original core rules.
The version I like is the 4th-level Bard ritual called "Song of Friendship". By spending 5 or 10 minutes, you can make a friend. You couldn't cast that in any sort of normal combat, but the performance might not be spotted if there's no one around who knows how magic works. The ritual is also very clear about what your new friend will and won't do for you (they won't go into combat for you). I would just take away the "bard" part.
Alas, there's also "Instant Friends", which drew hate when it first appeared, along with comments like "Oh great, they brought back Charm Person".
Black Tentacles (4) – battle breaker
I think this spell might have changed significantly from 3.5 to Pathfinder. While nasty (because the grapple check can get quite high), the victims do have a chance to escape without using magic, putting it in a better position than Hold Monster. Grapple values aren't very predictable in 3.x/PF either, especially the former. It's far too easy to either have DCs that are too low (and make the spell worthless) or too high (and make the spell overpowered).
Dimension Door (4) – story breaker
I think the best "nerf" would be to say you have to see where you're teleporting to.
Discern Lies (4) – mystery breaker
This one gives a save and has a short duration. The victim can also choose not to say anything. I think if you can force a person under this spell, you've already defeated them in combat or in a social encounter. (While the person might not say anything, silence could be considered incriminating.)
I've seen this spell in action, and it's actually very weak. (The 4e version has a longer casting time but gives a tremendous bonus. That prevents you from "ambushing" someone with the spell.)
Freedom of Movement (4) – battle breaker
It breaks grapple, but very handy when spells like Hold Monster are dished out. I don't know why it affects grapple, it really shouldn't.
Geas, Lesser (4) – can “dominate” for a week
Change the casting time to that of Geas/Quest. You shouldn't be able to dominate someone for a week with only a standard action.
Invisibility, Greater (4) – counterspell breaker
I agree with this one. The problem with the spell is the huge bonus to Hide/Stealth that it gives. This is a problem with the concealment/blindness rules (in that they're realistic, but that's not always good for a game) in 3.x, rather than a problem with the spell itself. In 4e, being invisible doesn't give you a bonus to Stealth, and it works far better ... but it isn't remotely realistic. (It basically turns you transparent, rather than invisible.)
Detect Magic takes three rounds to spot exactly where the hider is, and See Invisibility only helps one person. Invisibility Purge is probably the best counter, but the AoE is small, and you can launch Fireballs from over 400 feet away while invisible. There's non-magical counters (throwing flour, for instance) and Glitterdust, but that relies on guesswork. I agree that the counters aren't all that effective.
Restoration (2, 4=remove permanent negative level, 7) – death breaker
Players hate long-term negative effects like negative levels. It gets them to stop adventuring immediately. Quite honestly, if a necromancer wants to kill an opponent, they could just try to kill them. So to me this is a "get the players back into the dungeon" spell. I'd just as soon ban healing magic as this, and I'd never do that, because I'd end up with the same consequences.
Scrying (4|5) – mystery breaker
This is theory more than practice. The duration means you're never going to hear the "victims" talk about something plot-relevant, as what are the chances you get 18 or so incriminating seconds in a 24 hour-long day. You might literally get the victim sitting on the can. It can also be resisted, detected (with magic) and prevented (with Mordenkainen's Private Sanctum), a core spell whose existence I didn't even know about until after I stopped DMing 3rd Edition. While you can collect hair and stuff to boost the save DC, that creates an interesting submechanic. (Instead of the wizard doing all the work, you could get the rogue to try to steal their hair. And the rogue won't do that alone, as they're not suicidal...)
Stoneskin (4) – battle breaker
I don't think the amount of DR is ridiculous on this, but perhaps it should give lower DR at the start and gradually ramp up. I never actually see this spell cast due to the expensive material component. I had some experience with the insane Power Attack rules in 3.5, which meant NPCs shouldn't even bother casting the spell.
Dominate Person (5) – total control
I think the total control part isn't as bad as the duration, plus the unclarity of exactly when the victim gets extra saves. If you're going to dominate someone for hours or days, it shouldn't take a standard action to cast.
Dominate Monster is pretty much the same.
The psionic power Mass Domination was even worse (in 3.0). You could dominate 14 people for 14 days; even taking into account attrition from people making their saves that was broken. (Also, you could recover those spent power points in 24 hours, meaning any control after that time was literally free.)
Feeblemind (5) – spellcaster breaker
I hate spells like this. There are better ways of taking out a spellcaster, but this one includes a save penalty. I don't like this spell not just because it's use is so specific, but because you can cast it so quickly but it lasts forever. Seems more like a curse, and should be cast as a ritual. (This would take it out of any dungeon crawl game too.)
Flame Strike (5) – battle breaker
I don't see this as broken at all. It's Fireball, only you can only resist half of it. And it's higher level and covers a smaller AoE.
Planar Travel (5) – story breaker
Take a look at how 4e handles this one. When you gain the ritual, you gain the knowledge of how to travel to two specific places on two planes (places such as major cities, not random places). This is called out up front. Afterward PCs might try to find new coordinates.
Polymorph (5,7) – only if you get the special abilities of the creature
Fixed in Pathfinder. Even if you're not switching to it, I recommend stealing Pathfinder's polymorph rules.
Teleport (5,7) – story breaker
See Planar Travel above. Also note the long casting time in 4e means you can't use it to dodge battle.
Wall of Force (5) – battle breaker, counterspell breaker
The original Wall of Force was invincible. Now it has hit points, with with ridiculous hardness. I agree with this one.
Wall of Iron (6) – battle breaker
All it needs is clarity on Climb DCs. Make 'em balanced, if that's possible. I think PCs confronted by this spell give up since they assume they cannot possibly climb it.
Disintegrate (6) – save or “die”
Hasn't been save or "die" since 3.5.
Dispel Magic, Greater (6) – battle breaker
The problem isn't the spell but buffing addiction. I never saw buffing like that in 2e, which I presume was due to the spells not making much sense. (There was no naming of bonus types, and so people just got confused and ignored them, IME.) You can layer yourself in various buffs (requiring time to do math), then watch as half your buffs get melted again, then stop to do more math... Antimagic Field causes similar problems.
Forcecage (7) – counterspell breaker
Agreed. I think it's overpowered for the same reasons as Otiluke's Resilient Sphere (see below), so I'd make it a battle breaker as well.
I would also make this a battle breaker. You can cast it too fast, can call creatures that are more powerful than you (at least in theory), and there's not enough structure about regulating making a deal. How much do you pay? (I think the going rate is 1 XP = 25 gp, and please note that some creatures, such as elements, are weak for their Hit Dice cost. You have to pay an elemental more gp-equivalent than a solar.) How quickly must you pay? The duration of the spell is only 1 round/level and requires concentration, which should really make a deal impossible.
The spell can't decide if it's a combat spell or not, which I think is problematic. Combat spells shouldn't require an in-combat negotiation.
If the creature is a spellcaster, it can give you a wide variety of spells, including possibly Gate. (It's called, so it actually can summon stuff.) Any DM might say no, you have to negotiate extra for that, but the rules aren't clear at all on this.
There isn't really a 4e version as such, but you can replicate it using two rituals. Summon X (never mind the name, consider it Call X if you like), which is generally 15th-level, and Adjure, a 22nd-level ritual. The first just lets you summon the creature (use the Magic Circle ritual first!) and the second lets you control it with a skill challenge with clear rules. Presumably you're paying the creature with the ritual cost rather than directly expending it. In short, you're looking at Planar Binding, but with clearer rules than 3.x had, and I'm a fan of that. I'd probably render the summoned creature a companion rather than a regular creature (so you can heal it properly, and it's slightly weaker) but that's not really critical.
Summon Monster (1-9) - battle breaker. Messes with the action economy (rounds can take a long time*), fills space on the battlefield, and very flexible as to what exactly you can summon. (Flexibility is good, too much flexibility is not.) Being able to summon other spellcasters is problematic when it comes to game balance.
*For instance, you could summon 1d4+1 unicorns, each of which can cast Cure Serious Wounds once a day (3d8+5) and Cure Light Wounds three times per day (3d8+15 in total), and you have to roll all those d8s. Also, you get free Magic Circle Against Evil out of it.
Generally I find the summons to be weak in terms of raw combat potential for the level you can summon them at, unless you're a druid like my old Pathfinder character who can cast Animal Growth, and even then you often have to deal with damage reduction and stuff like that. They end up looking nice on paper but just waste everyone's time once they're actually there.
Otiluke's Resilient Sphere (4) - battle breaker. Much like Wall of Force. You can lock up a single creature inside the force bubble, ignoring spell resistance, and unless they've got teleporting or disintegration magic (or can deal enough damage to destroy a wall of force) they're stuck ... for 70 rounds minimum. I don't understand why anyone who hasn't banned Conjuration casts Hold Monster when this spell exists.
Simulacrum (7) - story breaker. Now that you can't apply metamagic to the spell, it's no longer a battle breaker. With this spell, I could create endless totally loyal copies, not just of myself, but of my friends. Or enemies. Or just people who impressed me with their skills. Quite frankly, even without the Disguise skill this is a bit of a story breaker. (The name and mention of the Disguise skill compels people to try to make good-looking copies, but many wizards couldn't care less about that.) I could make a simulacrum of the world's greatest accountant, get a decent one out of that, and now they have to work for me. The real accountant might be annoyed, but so what? I could create an entire organization out of these guys. I don't understand why villains in D&D modules don't use this more often.
I mentioned this in another thread, where someone wanted to say that wizards could not take over the world (because they're still individuals), but they're
not individuals due to this spell. Just hire competent bodyguards as well (eg friends) and you're fine.
Thing is, the spell's long casting time and material components probably balances it pretty well, I just think there should be a limit to how many of these guys you can have around (at least, how many
loyal simulacra).
Otherwise why isn't ever lich (who would have to disguise themselves with magic anyway, or some kind of mask) not creating a whole bunch of copies to draw fire, and copies of whoever to staff their organization, and not have to expend a whole lot of Charm Monster spells on them.
Sleet Storm (3) - battle breaker. It blinds victims in the AoE, already a nasty condition, and the victim doesn't get to save, instead they can just escape. All they have to do is walk out. No countering magic needed. Unfortunately they need to make an Acrobatics check, and since skill scores don't automatically scale in Pathfinder, you can easily run into higher-level opponents (say, the kind who wear heavy armor) who will only be able to move at half speed or even fall over while in the AoE. I consider this less balanced than Web, where the victim can make a combat maneuver check or Escape Artist check, and one of those is guaranteed to scale.
Mordenkainen's Disjunction (9) - omni-breaker. Magic items are such a critical part of balancing 3e that anything that destroys magic items needs to be looked at carefully. MD lets you destroy lots of magic items; it's like going through a capture scenario even if you kill the MD-casting opponent.
Also, there's no caster level check to strip off buffs. It's not level-dependent.
[As a by-the-way, I'm also using rituals to justify the low quantity of high-powered and "permanent" magic items (armor, swords, rings, staves, etc.) in my world : in addition to the feat, making each item requires a ritual, which can incur things like long-term Ability penalties and possibly death. So high-level spellcasters are only going to make items when they *really* need to.]
I always get worried when I see comments like this. 3.x just doesn't work with low items. Among other things, it disproportionately hurts non-casters. The system doesn't allow you to build AC at anywhere the same rate as attack bonuses either, so you'll end up with characters who can still kick butt but can't take it, which means they need to heal more, which they won't be able to do if you're limiting Wands of Cure Light Wounds...
