hi... i just moved from boston but i think i can provide a lot of insight. this might be jaded but where you might want to live depends on your age, what you want to do on weekends and week nights, where your girl will be in school and what is important to you.
here is my take:
if you want to live in quintessential "new england" and want to be near-ish to the ocean. you want to look in the "north shore" or "south shore" neighborhoods. you can look up on the web what their names are. north shore is north of boston and closer closer to the mtns (ME, NH, VT) and south shore is south of the city and closer to the cape. you might not think that being on one side of the city really matters but when you are trying to get to the other during rush hour, it really matters. so, if you dont need to be near the ocean but want that type of living, there is always lexington, wellsley, needham, natick and the like. none of them are cheap, all of them will require a commute.
if you want to live where all the college kids live and have tons of bars and be on the slowest trains (T as its called in boston), then you can live in allston/brighton. the pros are that there is always a place to eat, always young kids around having fun and there is always a bar to go to. the cons? the same as the pros. depends on what you want.
i would stay away from the south end and beacon hill. very trendy, very expensive BUT if you can afford it and are into the high end type of 'hood? those two cant be beat.
cambridge, 02138 - the most opinionated zipcode in america, is the best place to live IMHO. this includes cambridgeport, inman square, central square, harvard square and i will add porter square and davis square. those last two are in somerville but if you do live in one of those towns make sure you are walking distance to the red line. it will be the best move you ever made. its the fastest t line in boston and it gets you into the city in no time. also, it is right by interstates 95 and 93 and also super close to route 2 and the mass pike. those are all the north, south and west routes you need. also, the vibe there is great. funky i would say. no one cares what you are up to. the food and bars are great and you can go just about anywhere in those hoods in jeans and a shirt. the other places i listed, not so much.
parking is a bitch no matter where you live for the most part unless you are way out in the burbs or have a driveway.
i am sorry and dont mean to offend but i would not live in "southie". i have spent a lot of time there and it felt, to me, very disconnected from the city.
malden, waltham, medford and arlington and good places and people that live there are smart, but if you want to be on the redline or have a quick train ride into the city those places arent for you. again, just my opinion.
i vote davis sq.