Here's a list of my pet peeves, along with some suggested fixes:
Fireball vs. Lightning Bolt - long running debate, I know. My take is that Fireball is slightly overpowered, while Lightning bolts may be slightly underpowered. I base this off of monitoring real in-game situations with some sorcerers that have had access to both. In 99% of the situations, fireball is simply the better option. It has longer range and the ability to pinpoint it without having an open path to the enemy. A broader argument is that ranged burst effects will nearly always trump line effects if all other factors are equal.
To balance this, I'd first drop Fireball down to a medium range spell. Then for lightning bolt, I'd allow it to have 2 versions, the 120 line as it currently does, as well as a bolt from the sky (kind of like call lightning). The lightning bolt would be more precise, able to hit a single target in a crowd. Finally, I'd also make the lightning bolt have a slightly higher DC (maybe +2) for folks in metal armor.
Entangle vs. Web - Entangle has longer range and a bigger area of effect, yet is a lower level spell. Web has an advantage in duration, but during combat, it's not a big deal. Entangle doesn't always work depending on location, but then again web has a similar problem. Webs can be gotten rid of by burning them, but it's near impossible to get rid of entangle. Entangle just seems too powerful for a 1st level spell.
I would move entange to 2nd level, reduce it's range to medium and it's affect to 20' radius. Duration could be extended, making it comparable to Web.
Flaming Sphere - The spell is too wimpy because of the reflex negates issue. The sorceress in my monthly campaign has this spells and has tried to use it, but more often than not, it's worthless as the monsters make their saves and take no damage. I suggest either changing it to reflex for half, or making it work more like Spiritual weapon and requiring an attack (or maybe touch attack) each round to deal damage.
Hideous Laughter - There's a bard in both my campaigns with this, but it hasn't really gotten out of hand. Why? Most of the opponents are non-humanoid so they tend to get the +4 save bonus. It seems balanced with that restriction. But I can see in other campaigns where most foes are humanoids that this could be very abusive. To fix it further, I'd recommend that members of your identical race and sub-race get no bonus, but different sub-races get a +2 bonus. Members of different types still get the normal +4 bonus. I'd also make it mandatory to know the langauge of the target, otherwise, the target gets an additional +2 bonus on their save.
Now for some of the ones that I think are balanced but have been mentioned elsewhere in this thread:
Ice Storm - It lasts for 1 full round, damaging anyone that enters the large area of effect and it affects movement in that area for the entire round. It also has NO save. This is clearly better than fireball in many regards (ie rogues will actually take damage from it), easily making it a worthy 4th level spell.
Stat buff spells - Even after the 3.5 nerf, these are still good spells. They were WAY broken & overpowered in 3e. Too many folks seem to cling to the idea that these spells need to last longer to be any good. Playtesting in my own groups has shown that anything longer than 1 min/level makes them too good and they wind up being the only spells taken once again, which indicates a problem. Try out the 3.5 version, and you may be surprised how good they still are with 1 min/level duration.