I've noticed that rates can affect mic quality... try this: in console, enter the cvars rate 20000, cl_cmdrate 85 and cl_updaterate 30. I'm assuming you've got broadband, so these are broadband rates. You might not want to use these if you're on 56k.
Also... if the problem persists and you have tried different locations for the mic (refer to Slayer777's post), then you might have a hardware problem. Try using a different mic. If it persists, then you might have a sound card issue. From my experience, mic jacks seem to be the first to go for some reason. No clue why. In that case, you can just run to a Circuit City and buy a simple Sound Blaster Live! card to install.