I'm not sure what makes these spells "too powerful." They were put in there for a reason, after all.
I mean, take Polymorph Other. Like m&m pointed out, no one use of it is powerful, but it is very versatile...however, your average mage, when he can cast it, can't make use of that versatility because they can only cast it once. One spell=one form. I'm not sure this needs a seperate spell for each form, since you have to cast the spell every time you want a different form. The biggest advantages are that you can choose what to do at the time of casting, rather than at the time or memorization (for wizards), and that the one spell can take the place of others you'd have to learn (for sorcs).
I've never had a problem with any of the spells in the PHB...I've been gaming for a good number of years (though, admittedly, many of you have had more.

And only 3e since it came out...), but that tells me that if, say Glitterdust, was that godawful powerful, that the mages I've played and DMed would've gotten their hands on it as soon as they could...
...they almost always go for Melf's Acid Arrow instead. Or one of the ability-increasing spells. Glitterdust? Why wast precious known spells ('cause even Wizards are limited by DM capriciousness as to how much they know) on something that a druid's animal companion or your familiar can do for free (*sniff**sniff* Find the invisible critter, boy!) when you can spend them on things no one else can do in a non-magical way (like blowing stuff up or helping the fighter live a bit longer so you can make your escape).
I dunno...I've never heard of anyone describe an in-game situation to me in which these spells have become unbalancing or too powerful. Maybe if/when that happens, my opinion will be revised. But I haven't seen it...
As for the actual question, I believe another poster hit it on the noggin: Spells are balanced by class. You've gotta take the whole powers of the class into consideration when you're designing a spell list, not the spell list only. Why to Wizards get Fireball or Mage Armor? Because without them, they're walking around unable to deal or take damage...big walking Orc Buffets.
