I'm going to use this one:
http://www.amazon.com/Audio-Technica-AT2020-USB-Condenser-Microphone/dp/B001AS6OYC/ref=sr_1_2?ie=UTF8&s=electronics&qid=1275750077&sr=8-2
It's not the best quality you can get, but it works fine.
USB microphones work fine. The only problem that someone might have with them is there is some latency. So if you were to record a band one instrument at a time, it would be hard for them to keep tempo because of the latency. But if you would just be sampling pipe organs with this microphone, then you don't need to worry about that.
I haven't read much about this microphone, but it should be fine. It's probably better than mine