I'd like to put in a plug for Window on Rome, where we stayed for 2 nights. It's in Trastevere, very close to the Tiber, so it's within walking distance to the Pantheon, the forum, the coliseum, and almost all the major tourist sites. Window on Rome is a small place, just a few rooms, but they are clean, well maintained, have a/c, and, being on the 5th floor of the building, they have excellent views. The rest of the building is, I think, just private apartments and another guesthouse. Guests also get access to the roof terrace, which has spectacular views in the evening. The innkeepers are a charming couple who live on the same floor.

We stayed in the two bedroom apartment, which wasn't quite as spacious as it sounds (there was no separate sitting room, but there's a nice little kitchen), but still plenty for 3 people.