Wiki lists 21 neighborhoods and I think us locals have opinions and preferences regarding each one. Some I would rule out NOT because they are bad neighborhoods but because I don't see many listings there, which means other providers have chosen not to set up shop there. Some I would rule IN because of lots of nice hotels, convenient public transit (the "T"), just a short-hop taxi fare from downtown or available and affordable parking.
1. Allston/Brighton - No. Too far out.
2. Back Bay - Yes. lots of plusses: "T", parking, hotels, ...
3. etc.
In the suburbs, Metrowest is often mentioned probably because the Mass Turnpike (Rte 90) easily gets you to Rte 128 and beyond. I don't do that commute, but I guess that guys find it convenient to go to Newton or Waltham (Rte 128) and take their "detour" there before getting back on the Pike or 128 to head home. Or, from 128, they head North (Burlington ...) or South (Dedham ...) to their "rest stop" before heading home.
Some people may mention districts within neighborhoods that are also popular: Theatre District is close to Chinatown and is a good choice. But Leather District, also near Chinatown, doesn't have the hotel options.
Per usual, Foodguy and Mr Fisher have come up with some good advice a lot more succinctly than my spiel