If you have FFDShow installed (which I recommend - I use it myself) you should have no other Divx or XVid codecs installed. Multiple codecs for the same codec type only cause problems.
On all my personal systems I have only FFDShow and AC3 installed.
You can run DxMan which shows what codecs are installed and lets you individually uninstall them:
http://www.analogx.com/contents/download/audio/dxman.htm
You can also use GSpot to see what codec is being used when you run a specific video file:
http://www.headbands.com/gspot/
The problem may be WMP which I personally despise and never use. Try another player just to eliminate that possibility. I HIGHLY recommend the free version of BSPlayer. It's what I use for all files except Real Media and Quicktime (I use Media Player Classic with Real Alternative and Real Quicktime instead of those two bloated adware monsters):
http://www.bsplayer.org/
If it stutters in BSPlayer then I'd say it's a codec or driver issue. If it doesn't stutter in BSPlayer I'd say is a problem with WMP. May need to re-install it (or better yet, forget about it).
Are you running WMP 10? If you're still running WMP 9 I'd upgrade to 10 (just for the codecs even if you don't use it) and since it will replace practically all the WMP core files that may fix it.
If it stutters in any player you try then I'd look at video and sound drivers next. Make sure you have the latest ones from the manufacturer, and not hacked drivers.
Another possibility is that there's a background app either interfering with video playback, or just stealing a lot of CPU cycles. Watching Processes in Task Manager might give you a clue.
Wouldn't hurt to perform a thorough spyware cleaning. Please refer to my detailed spyware cleaning instructions here:
http://theflyingpenguin.com/spyware-removal.shtml
Another possibility is some tweak you may have enabled for your video card may be causing problems. Also if you've changed the AGP Aperature setting I'd recommend setting it to the default of 64Mb to see if that fixes it.
Hope this helps...