For museums, most around here are overwhelmingly large and pretty much standard museum fare. The real jewel is the smaller http://www.gardnermuseum.org/ . It's in a big old mansion and has an amazing collection and cafe. Also, the Boston Public Library is right in the middle of town (and near Newbury St.'s shopping) and is a neat old building with rooms full of murals and whatnot. It also has nice clean bathrooms!

You can get a subway/bus pass for a week from the pass machines inside the stations, they just went to a different system than you'll probably find in guidebooks and I believe it's a lot better for visitors. If you can, try to avoid the Freedom Trail on Saturdays- it's a zoo. The North End is neat and improves greatly if you venture off of Hanover St. and find all of the tiny Italian meat markets.