My problem is when I play counterstrike source or any other game it seems to skip and lag, kind of like a hiccup. When I walk the floor shakes like crazy. I wish I knew what the problem was. Here are my specs.

NVIDIA 8000GS
1000W Toughtpower
ASUS P5Q deluxe mobo
6600 @ 2.40ghz 2GB RAM

Does this problem occur e mediately when you start up the game or does it take some time before it starts, also by floor shakes you mean the textures in the game are going all crazy like?

Yes to both of your questions

I went from a 2900 XT ATI 1GB to a 8800 GS Nvidia

Although you are above the Minimum specifications for the game
Your Video card is only 384MB, and 2.40ghz (single core?) is a bit low

I tend to disable as many startups as possible, here's a good tool for that: http://www.mlin.net/StartupCPL.shtml
And run CCleaner regularly: http://www.ccleaner.com/download/downloading

Actually if you have an exit on your Antivirus or 3rd party firewall, I'd do that as well (whilst playing offline of course)

Or consider upping to a better faster computer for gaming
Which Windows OS are you running?

Yes I went from a 2900XT 1GB to a 8800 GS I had the same problems with both.

So you dropped Memory on your Video card?

Yes I dropped memory because even with 1 GB on my 2900 nothing changed when i switched.

6600 @ 2.4 I'm assuming is a E6600 which is a dual core not single in which case thats fine for gaming and more than enough for CSS. Try doing a complete uninstall of your current video drivers and then boot up in safe mode and run a program called Driver Sweeper to get rid of any left over files, reboot, then install the latest drivers that you can get directly off of Nvidia's web site. If that that doesn't fix it then there may be something else wrong.

Ok I will try it and see what it does.

Driversweeper:

Restart

nVidia Drivers: