Mac has mini freezes for 5+ seconds

Hey guys, I searched pretty well before making this so sorry if I missed another thread!

My problem isn't really crucial, just annoying.
It started when I had my hard drive fail and then had a new one put in. I've since been fixing small system errors and such from corrupt files. But what happens about once every 3-4 minutes I'll either be typing, watching a video online, playing a game or anything and my MBP will freeze for about 5 seconds then go. If I'm typing the letters stop being inputted then once it goes they all jut out at once. If I'm watching a video the audio will continue but the video will freeze, and if I'm playing a game the game will all together stop for the 5 seconds then take off. I've run Tech Tool Pro and Disk Warrior on it to try and fix it with small improvements but still not fixed. I used my install disk to repair a bad directory of some sort and now neither TTP, Disk warrior or disk utility can find anything wrong. I also cleared my ram at start-up with no change either. So if anyone could shed some light upon this I'd greatly appreciate it! Thanks!

Update: Just for the fun of it I installed Windows xp on a small partition to see if it happened on the Windows partition and it doesn't so I think it's linked to the mac side. After that I wiped my hard drive and re-installed Os x with no luck. One thing I've noticed though is that my Hard drive revs up and slows down quite often and I'm not sure if that's normal? Perhaps this issue has to do with it catching up. Though it's a brand new hard drive and my old one never had this issue. Any help would be great guys I'm losing my mind here.

Here's my specs:

Mac OS X 10.6.4
2.8 ghz intel core 2 duo
4 gb ddr3
500gb HD

Update

I've been reading a lot about faulty hard drives and mine almost makes the cut. Mine will click and rev up quite often and I'm wondering if I just have a wacked hard drive? The only thing that's throwing me off is when my mac does freeze for the 4-5 seconds and if I'm watching a video or playing a game the audio will continue and the video is the only thing that freezes along with any mouse/keyboard input until the freeze is over. Has anyone else had similar hard drive issues?

Thanks again.

Bump, I need help!

Hi,

I have the same thing happening to me. Even weirder, I can be typing, and the characters are buffering somewhere, BUT in order for them to appear, I have to re-click in the text box where I was typing.

So either the mini-freeze or mini-slowdown takes the focus away from the text box, or it's something I have no clue about.

Things I've tried so far:

Put in a new drive (Momentous XT Hybrid) (Nope)
Dropped Safari in favor of Firefox (Nope)
Ran DiskWarrior multiple times (Nope)
Tried running with no external USB connected (Nope)
Cleared out disk space, now have 130G from 500G free (Nope)
Tried running with no login items ON (Nope)
Now defragging drives with Tech Tool Pro ....?

Have either of you ran Disk Utility to verify the disk? How about Permissions?

If you haven't, click on Finder>Applications>Utilities>Disk Utility