The Charles Hotel, just off Harvard Square, is a gem. The rooms are beautifully appointed -- there's even a tv built into the bathroom mirror! -- and the staff couldn't be more helpful. The two restaurants give you a range of choices, and out on the plaza (that the hotel overlooks), there's also a Legal Seafood. If you like jazz, the hotel is home to the Regatta Bar, a great venue. And of course you can spend hours walking around Harvard, visiting numerous shops, galleries and museums. We stayed there as a little romantic getaway after attending a play at the fabuous American Repertory Theater, just a few blocks away.
And of course, if you want to hop in your car or take the T, you can be at a number of other popular squares (Porter, Central, Kendall) in just a few minutes, not to mention MIT and, across the Charles River, Boston. Surprisingly inexpensive, given Boston room rates, but don't tell them I said so.
FYI: We didn't use the spa, so no rating, but we've heard it's great. There's under-the-hotel parking, which is very convenient, and even a "juice bar" if you are one of those enlightened folks who drive an electric car.