it depends on the kind of scene you're into but one of my favorite places in the city is The Middle East. If you like rock/alt. music it's awesome. The Avalon is cool too, but that's more of a dance type of place. I know MSN has a really good listing of clubs/bars/nightlife. If you Citysearch Boston, MA and look at the Cityguide for Bars & Nightlife, there's about 12 sub-categories to look through. Most with their own websites.
Have fun! Boston is a GREAT city!
