I've been here for 3 years now so I can help a little. What are you interested in? A few quick thoughts on what you listed - Click the names for location maps.
Good Bars If you're going to be staying in Boston proper somewheres, I have a few favorites but as a married man with a 7 month old, I don't get out much anymore.
Bukowski: This a great little dive bar with TONS of good beer, and I mean about 100 in bottles and 30 or 40 on tap. The music is loud, the bartenders are nice, the server girls are cute and tattoo'd, and there are very few douchebags / massholes there... the music drives them away. It gets crowded early but the beer selection and the lack of meatheads makes it worth it, to me.
Black Rose: If you want the authentic boston irish bar experience, this is a good way to go. 'Nuff said. Also I LOVE JJ Foley's in the south end, but just because of living near it, probably. You wouldn't be all that impressed.
Restaurants Do yourself a favor and make it down to the South End. I'm only a little biased by having lived there - it really is where most of the good, local, fresh, killer places to eat are these days.
Gaslight: This is our favorite place right now, it's a killer french sorta brasserie place. It's just below sidewalk level with lots of windows, the decor is perfect early-1900's white subway tile kinda stuff, the food is very very very good, the service is top-notch, it's not too cheap but it's also not like super pricey. Like, less than $20 a plate for most things. Trust me, it's worth it. We've always had a great dining experience there. They get it right.
Meyers & Chang: Great fresh asian food, not awfully expensive, neat decor and easy location to find, right off a silver line (bus) stop. The pork dumplings are killer. Also try the Pork Slap beer if you've never had it.
Touristy stuff / Museums The Museum of Fine Arts is big and amazing if you're into that. Walking the Freedom Trail can be fun if you're into history. I always take guests walking around in Little Italy - it's small, you can only get
so lost, and it's chocked full of good food and groceries. Paul Revere's House is there too and it's a really interesting thing to walk through, I do recommend that for sure. If you're up for a quick subway ride north, Harvard Square is a lot of fun to walk through. You can shop, walk the college grounds, and go to the surprisingly kickass Natural History Museum there too... dinosaurs and whale skeletons and so forth, kids dig it too. And if you're into walking, and the weather is nice, you can walk along the Charles River on either side along the Esplanade. It's a paved walking / biking path that's right on the water, and goes for a few miles. Great place to take a picnic lunch.
Like I said, if you tell me more about what you're into, or what you've already seen, I can probably help some more. Either way, WELCOME.
A tip: if all the bars are jammed into the street and you are starving/thirsty, you can usually get a table without much/any wait over at Jillians bowling alley (Lucky Strike Lanes?) up on the 3rd floor. Nice facility with plenty of big screens and ok food if you stick to the basics like pub burgers and such. But you lose out on the "street scene"...no biggie though there will be plenty of entertainment inside the stadium 
