If you're going to do analog transfers to your PC from your MD recorder (and it sounds like you'll have to), the most important requirement is a quiet sound card. I have an M-Audio Revolution PCI card, which cost about $100 and is designed specifically for low-noise recording (they also make a USB version). I just run a stereo mini-plug to mini-plug cable from the line-out on my Sharp MD's docking cradle to the line-in on the sound card. I usually record into Cool Edit Pro @ 44.1/32 bits, but if you don't have a good audio processing program you can still get acceptable results recording into the downloadable freeware program CD Wave, which also makes short work of slicing the recording into tracks for burning to CD. It won't be any help if you need to do EQ or other post-processing, however.
It is a good idea to keep other activity on your PC to a minimum while recording to avoid dropped samples.