Seems you've already got a bunch of suggestions here, Block, but I'll add a few...

I really like Harvard Square and if you're only going to have a short time here it's one place where you can walk around and see or hear a lot of different stuff.

There's Passim which is a folk club right in Harvard Square. It's always worth checking out who may be there at any given time. A bit outside the Square headed up Massachusetts Avenue toward the city is The Middle East, which draws all sorts of music and is probably thought of as Boston's coolest rock club.  When you are in Harvard Square you can try John Harvard's which is a brew pub there, it's a chain now but I think this was the original. If you want a cheap sandwich and a brew you can try Grendel's a Harvard Square it's been there forever. Our House of Blues used to be right across from Grendel's...it's gone now they turned it into a bbq joint. It was the only House of Blues that was really a house. From the Square it's a short walk over to stroll along the Charles River. You get the best views of the city from this side of the river (the Memorial Drive side...the People's Republic of Cambridge is on the opposite side of the river as Boston proper). It's a nice walk on a summer night.

The best major concert venue in the city (it was once voted one of the best in the country) is the Bank of America Pavilion on Boston Harbor at Fan Pier. It's a short stroll from the Tea Party ship and the Aquarium is near by as is a Legal Seafood restaurant. There's also a restaurant called The Barking Crab right there that is popular with folks going to the Pavilion and the No Name restaurant is right there on the fishing pier and legend has it has always been the best seafood restaurant in town. Just so you know Lyle Lovett is playing there the Friday you are here and Elvis Costello on Saturday. Don't know if either of them interests you but the B of A Pavilion really is a great outdoor concert venue right on the water. If you have any interest in those guys I'd get tickets and go see them there.

I also like Harper's Ferry, a blues bar in Allston on Brighton Avenue...

If you are downtown Newbury Street is trendy and expensive but not bad for people watching and I will admit I've been caught sitting in some outdoor cafe there on more than one occasion. Lansdown Street is one big club area and a place I always avoid. It's right behind Fenway Park and draws a young crowd.

So there are a few thoughts...