Poly Other is probably the poster child for problem spells. As an offensive spell, alone, it's good enough to be 4th level. As a 'buff,' alone, it's insane. And, it's /both/.
Nothing else is quite that bad. Yeah, Harm is nasty, but, by the time it shows up, Heal & Raise Dead are availble - it's just another way that you can die at any time, at any level, in 3E, but, hey, you can come back, too. Haste is a potent spell, especially with the ability to cast that extra spell every round - but, that's also it's weakness - casters who avail themselves of two (or even three) spells/round go through spells that much faster, which can make a 'busy day' (multiple encounters between recharges) very bad for them.
I'm sure Spikes and plenty of other spells from suplements are 'problems' - but, realy, the PH spells & classes should be enough to keep a group busy for quite a while, so the easiest 'fix' is just to decline to use them.