These are two that might be well known, but I don't really hear people talking about:

• I use Map Genie quite a bit. It's just a bunch of interactive maps for a lot of different games, but it's really helpful when looking for that one item you're missing, or waypoints in general. It's mostly geared towards open world games.
• I also use How Long To Beat if I looking to play a new game but don't really want to spend over a certain amount of hours playing. (Although I'm a bit of a slow player, so whatever completion times are listed I have to multiply by 2).

The other reference sites I use like NeoSeeker and Game FAQs are pretty well known and have been around for ages.