I'll list only places not already mentioned by other folks.

100 Flowers Bookstore in Central Square. Left-wing books for a left-wing city.

The Book Case, on Church Street in Harvard Square. Cheap used books piled floor to ceiling in multiple rooms on both sides of the street.

Bookcellar Cafe, a used bookstore in the basement space now occupied by McIntyre & Moore Books in Porter Square.

Barillari Books, where FedEx-Kinko's is now on Mt. Auburn Street in Harvard Square. Sort of a clone of WordsWorth.

Cambridge Booksmith, on Brattle Street in Harvard Square; same owners as the current Brookline Booksmith.

Reading International at the corner of Brattle and Church Street -- now American Apparel. Huge selection of obscure magazines from all over the world.

Off the Wall Cinema in Central Square.

Orson Welles Cinema between Central and Harvard squares.

The original Steve's Ice Cream in Davis Square (torn down to build Carberry's, now Green Tomato II)

Grand Prix Cafe on Mass. Ave. near Day Street, just closed last year.

Filene's.
Filene's Basement, the original one downtown.
Jordan Marsh.

The John Hancock Observatory.

Elsie's Lunch in Harvard Square (on Mt Auburn St, now a Boloco)

The old, larger Grendel's Den, with semi-outdoor seating and a view of the street scene.