Most of the Joie de Vivre hotel properties (
http://www.jdvhospitality.com) would be good candidates, and tend to be good value. I've stayed at the Andrews, the Maxwell, and Hotel Rex, and would recommend any of them. The Andrews (
http://www.andrewshotel.com)is a particularly good value, has an excellent restaurant (Fino) in the lobby area, and is quite small (48 rooms), ensuring personal attention. Breakfast is in the form of a tray of pastries, fruit, etc. placed in the common hallway area on each floor. The rooms are small, but nice. The largest, most expensive room in the hotel (the Petite Suite) tops out at about $179, and you can get a perfectly comfortable room with a king or queen on the street side of the building for less than $140.
Kimpton Hotels (
http://www.kimptonhotels.com) also runs a number of SF properties; these tend to be a bit pricier and more luxurious than the JDV properties, but with a little searching you should be able to find something in your price range without too much trouble. The Prescott on Post Street (
http://www.prescotthotel.com) is a particular favorite; Postrio, a Wolfgang Puck restaurant, is inside the hotel, and I love the "living room" area off the lobby with its huge brick fireplace. It would be an excellent romantic choice for a honeymoon night. I also really liked the Serrano Hotel (
http://www.serranohotel.com) on Taylor Street; a little bit funkier than the Prescott (they have a thing about board games, scattering them around the public areas of the hotel and maintaining a library of them for guest use at the front desk -- not that you're likely to use them on a honeymoon). It's a little bit farther from Union Square, getting close to the Tenderloin, but otherwise it's just as luxurious and accommodating as the Prescott. I haven't stayed at the Sir Francis Drake since it was renovated and Kimpton took it over -- it's a big, old hotel, in a great location. With Kimpton running it now, the service and appointments should be high quality (not the case in previous years when I stayed there); it's a landmark and a local legend, and the doormen in their Beefeater regalia are kind of quaint.
I was extremely impressed with the Argent Hotel (
http://www.argenthotel.com) during a stay last summer -- so much so that I booked a stay there for my wife and I the weekend before July 4 this year for an anniversary trip. It's a large hotel (nearly 700 rooms in 36 stories), but I was quite impressed with the quality of service, the appointments of the room, the view, etc. The location is excellent as well, just a half-block off Market on Third. I think it might be best overall value in the SF hotel market right now for Union Square/Market Street area properties.
