Hi Zack,
I've heard many favourable reviews of GoTryThis. Personally, I haven't tried it, but it seems extremely feature rich and definitely a must for serious affiliates.
If you're looking for something basic, I've actually written a lightweight link management script called Simple Link Manager. If you'd like a copy (it's not available to the public yet), just send me a PM. It's nothing fancy, but it gets the job done.
You can take the demo for a test spin at
http://demos.telidesign.com/slm/ .
~ Teli