so far the most likely cause is adobe flash player. flash player for os 10.7 is still a beta, [flash player 11] I tracked it down via a strange kernel message that was spamming the logs like mad. uninstalling flash player seems to have greatly increased lions proformance, but I'm still having a few stalling issues from time to time but nowhere near as severe. seems flash is only part of the problem, although a pretty big part. here is the fix so far and what I have been able to determine.
flash player 11 beta is causing a large number of strange kernel messages, sometimes hundreds per second or more. I'm not sure how or why yet but it's a major contribution to read/write stalls with mac os lion. the read/write stalling out leads to incorrect permissions [or incomplete] being written as well as ocasional hard drive errors which further contributes to the slowness [which is why perm fix and scans seem to give temporary speed boost] this by far isn't the only problem, other programs have been generating similar kernel messages and causing mac os to stall on drive read/write operations but not as severe.
current steps to help increase your macs proformance till these issues can be solved by apple and or adobe are as follows
download the uninstaller for flash player here http://kb2.adobe.com/cps/909/cpsid_90906.html I know it says the uninstaller is for up to 10.6 but it still works fine on 10.7, this will remove the flash plugin. Don't reinstall it till it's been fixed by adobe unless you want your comp to go slow again 😝
step two, boot your mac while holding the alt/option key and you'll get a boot menu, boot to the recovery drive and run disk utility, repair your macs drive and fix permissions, even if it doesn't display any errors found for some reason it still helps.
final step if the above two steps don't fix your problem, open a terminal window and follow these instructions posted by rich cook, it'll disable all the automatically launched background stuff that mac really doesn't need. you can restore the ones you do need later.
sudo mkdir -p /Library/LaunchDaemons/disabled
sudo mv /Library/LaunchDaemons/*plist /Library/LaunchDaemons/disabled
sudo mkdir -p /Library/LaunchAgents/disabled
sudo mv /Library/LaunchAgents/*plist /Library/LaunchAgents/disabled
good luck.
ps, for me, uninstalling flash and the drive checks was all that was needed, final step wasn't needed. your own milage may vary, I'll continue researching this problem and provide more information and/or better fixes as I discover them.