same problem here, spotlight fully indexed, permissions fixed, pram smc both reset/clear, no hard drive errors of any kind, in fact it's a brand new drive, a hybrid ssd that supports osx just fine.
I originally installed this drive with 10.6.7 with blazing preformance increase, 10.6.8 killed it. constant freezes and system lockups. 10.7 is at least stable for me, but it's so horribly slow it's just rediculus. Apple broke something major for lion, and imposed same change in snow leopard 10.6.8, and I'm betting it's relating to the way it manages the hard drive. it's stupidly slow and then some.
and for all the basic questions that follows of everyone who thinks they're right......
no there's not a lot running, yes I'm virus free [for those who would suspect such a thing] no there's no fancy 3rd party stuff, yes I have 4 gigs of ram, 2.4 ghz 17 inch macbook pro. only thing not stock in it is the hard drive and I only installed it cause apple care plan ran out like a month before my drive kicked the bucket. and you can skip 90% of the other basic trouble shooting steps like clearing caches and maintiance scripts and so on.
I suspect I might be able to solve the problem by pulling the sata driver related files from 10.6.7 and overwriting the new ones. not sure. all I know is lion wasn't ready, it shouldn't have been released till full regression testing was done on all mac models.