Spells that "break" the rules:
Discern Lies/Zone of Truth:
The game breaker aspect is that suddenly, all the ranks invested in Bluff or Sense Motive are useless. Just use the spell to make the first one unimportant and the second one not required.
This is simply a matter of wording. You can answer any question truthfully, by not answering with a lot of truthful information that doesn't really answer the question; if such a question were to actually be asked, in such case as an answer can be given if possible.
Teleport:
Suddenly, the group doesn't have to travel to a place (no more wilderness encounters for you - which might not be that bad). But the most important game breaking element is the combination with "Scry" - suddenly you can get to your enemy anytime you want.
I never understood the trouble with scry. There are simple spells that can make things un-scryable? To me, this is a perfect way to set traps for your party, it lets you set up an ambush where they thought they were being smart.
Speak with Dead:
Just ask the victim who it was. Solves most murder mysteries, unless you always have a story that ensures that the murderer wasn't seen by the victim, or the murderer was disguised or controlled by someone else. (Meaning the case is a bit more contrived than usual.)
See the zone of truth response.
Save or Die spells*:
Suddenly, all the hit points you might have had become meaningless. The classical safety net is gone. A single roll decides whether you get to live or die, and you don't really have a way to defend yourself against it.
Possible Fix: See Disintegrate and Harm (deal massive damage), or Power Word spells (only targets with X HPs or less are affected)
*) There is also the category of Save or "Suck" - depending on the degree of "suckness", you can put them in this group, too. Save or -4 to an ability, Save or 50% miss chance are fine, in my view, but Save or become a frog or Save or be paralyzed for the rest of the encounter are not.
These are good spells, and not unbalancing at all. In general, no character should be invincible, and with all the cheese added to characters today, they are nearly so. It's a spell of luck, and no more unpleasant than attacks of opportunity which can be equally deadly with the same amount of luck. Besides, with resurrection and true resurrection, what difference does it make?
Dominate Person/Monster:
Even better than Save or Die spells: Save or get the enemy of your friends. Instead of taking just out one enemy, the caster just also "summoned" an ally.
On the other hand, the spell has great flavour element and is a typical fantasy trope:
Possible Fix: See Save or Die Spells, and also make it harder to use within combat (either the "ally" will have a very easy time to resist commands, or it just takes longer.)
Nothing a creative DM couldn't cope with.
Magic Circle vs Evil:
The +2 to AC and saves is fine. The immunity to charm and compulsion effects not so much. Essentially, you completely negate the ability of many characters and monsters.
Possible Fix: Reduce the benefit (and in turn ensure that compulsions and charms aren't getting to strong, see Dominate Person/Monster)
Again, one simply has to draw them out of the circle. Either they do something agressive to negate it, they sit back doing nothing but buffing, or they move the circle onto an npc, or they watch their party die. All of these limit what the player can do bringing balance.