A few ideas:

eMusic.com - requires a subscription, but has excellent prices and a wide range of folk, trad, roots music. (I've been happily using this for a year and a half and gotten a lot of great trad music from them. I always look here first because of the much lower price.)

tradtunes.com - Irish and Scottish and some English music.

Smithsonian Folkways site - You can buy CDs, or download tracks or whole albums of folk and world music.

eFolkmusic.org - I haven't tried this yet myself, but it looks like an interesting source for folk downloads.

Amazon.com has just started an MP3 download section this week, especially focused on independent labels, where most of the trad music is. I haven't had a chance to really explore it, but there should be some trad there.