Places to see bands, in no particular order: Church (Fenway), The Midway Cafe (JP), McGann's (North End), The Precinct(Union Sq. Somerville), The Middle East (Central Sq. Cambridge), The Cantab (Central), All Asia (Central), Ryle's Jazz Lounge (Inman Sq. Cambridge), The Lilypad sometimes (Inman), a ton of other places in Allston, Great Scott, Brighton Music Hall etc. As well as the usual suspects like the Paradise Rock Club, House of Blues etc. Most of the bars have live music on the weekends.
As for comics, there's always Newbury Comics, and you can find smaller gaming/comic stores here and there as well. I believe there's one on Mass ave across from the Christian Science reading center, near Symphony, and I know there's one in Davis square as well.
I don't really buy coffee so I can't help you there. Redbones in Davis Square is the best BBQ anywhere around the city, McKenna's in Dorchester is an amazing breakfast/lunch/coffee place. South Street Diner near South Station is open 24 hrs unlike basically everything else in the city, and Victoria's on Mass ave near South Bay Center is open 24 hours on Thurs/Fri/Sat.
Good Bars by location:
Cambridge: The Middle East, Bukowski's (awesome), Christopher's, some others, but those ones are solid.
Allston: The Sunset Cafe/Cantina (has more beer than you can possibly imagine, good food, mead, good drinks etc.), The White Horse Tavern, I guess Wonderbar if you like a more club-ish scene, but it's not for me.
JP: The Brendan Behan Pub (just a no-nonsense small Irish bar. Home to basically anyone around Hyde Square), The Midway Cafe (exceptionally divey)
Dorchester: Savin Bar & Kitchen, the Harp and Bard
Somerville: Underbones (bar under Redbones), The Burren, The Precinct
Good luck! Be warned, things close unfortunately early in the city, the T especially.