I recently put together a new computer and I've run into this issue in every game and every application which uses 3d acceleration.  Here's what happens:

The application will run smoothly for a period of time, say 3-4 minutes.  Then it will 'catch' -- a little delay, run again for 1-2 seconds, and delay again.

There are always five of these catches in a row, followed by another period of running smoothly.

During the stuttering, there is no disk access being performed, and it happens even in older games or at lower detail settings with which the video card should have no problem.

After searching around, I have found people with similar (but different) problems and have tried the following solutions to no avail:

Disable V-Sync
Disable "Cool & Quiet" in the BIOS
Disable Windows DEP
Disable all On-Board features (LAN, sound, graphics) in Windows
Disable all On-Board features (LAN, sound, graphis) in the BIOS
Set "PCI Bus master" to "PCI-Express" in the BIOS
Change NVIDIA Tuner settings from "High Quality" to "Quality"


None of these seem to have worked, although I thought that disabling DEP + On board features did work for a while, since after I rebooted games seemed to run fine.  However, I came back today and the issue has returned.

Right now I'm investigating if perhaps the graphics card is overheating, but I don't think it is.
Edit:
My video card seems to max out at around 79 C and run idle around 56 C. That seems rather hot. -- should I invest in another fan?
/Edit

Could this be a hardware problem? A driver problem?

I found this thread, but this issue appears to be for AGP cards and none of the solutions posted worked for me.



Here are my system specs:
AMD Athlon 64 3200+
ASUS A8N-E Motherboard
1 GB RAM
Nvidia GForce 6600 128 MB RAM (Latest driver)
Windows XP Professional x64.

how many fans are in the tower?
Does the internal heat sensor read a normal temp.?
Do you have the luxury of haveing a second computer to test it with for a cupple days? (differant OS)

[quote author=l)ragon link=topic=14405.msg147455#msg147455 date=1141342335]
how many fans are in the tower?
Does the internal heat sensor read a normal temp.?
Do you have the luxury of haveing a second computer to test it with for a cupple days? (differant OS)
[/quote]

1) I just have one case fan.
2) Not sure what you mean.  Here's what I've got:
Mobo Temperature: 39 C
CPU Temperature 40 C
Power/Aux Temperature: 25 C
3) I guess I could take it to work and throw it in my Linux box there for a couple days and play around with it, but that would be pretty inconvenient.

Edit:
I just started up a game and the Video Card temperature shot up to 82 C pretty fast -- that's way too hot.

You should probably try to RMA the card. That kind of failure has got to be a manufacturing defect -- bad thermal transfer between the GPU and its heatsink or a dead fan on it or something.