Your results may vary, but I've been able to use milkdrop with a combo of winamp and MC.
The plan is to use this LINE-IN plug-in for winamp:
http://www.winamp.com/plugin/linein-plugin-v1-80/84040This plug-in lets winamp run milkdrop from the line-in jack on your soundcard/mobo.
With a stereo mini-jack (3.5mm) patch cord, connect the line-out of your soundcard to the line-in. Do not forget to adjust the gain so that the input won't clip. I don't know if this is really a safe practice for your hardware, so don't blame me if something bad happens.
You can create a second zone in MC, so that your primary sound output is not sullied by the I/0 loop you've just created. Link this secondary zone to the primary zone in MC, and change it's output to use the line-out. Open winamp, and with the line-in plugin installed, press cntrl-L in the main window to "open url" of:
linein://
Milkdrop now kinda works. You still don't get text overlay of track info, but it seems to look good on:
win7 64bit on ssd
4gig ram
amd sempron 2.8
1gig ddr3 nvidia w/ hdmi @ 1368 x 760
with:
winamp v 5.622
milkdrop v 2.24
MC v 17