You probably have a bad hard drive or a bad cable. Both can produce similar symptoms. Another possibility is that you might be loading some kernel extension or app at boot time that's causing problems, but on Lion the bar moving across the bottom means the drive and it's indexing is being checked, so I have to assume the problem is most likely drive related. Before doing anything else I would back up the drive if that's possible.
To understand this type of problem you might want to look at this link:
Hard Drive Problems
Look in the section on general problems.
Assuming the drive or cable is bad, to see what it takes to fix it, take a look at this site:
Assuming the hard drive is the culprit, I would recommend an Hitachi as a replacement:
They make a really good 7200 RPM 2.5" drive with a 32MB buffer and a lot of places are selling them for about $50 U.S..
Most of my post is assuming the drive or cable is going bad. After backing up you might want to try to boot into safe mode and see if the problem persists. If it doesn't then there's an app or kext file in there somewhere causing problems.