For me I think it's videos. To see how the Masters actually think when they are working through a problem is very helpful to guaging what I should be thinking about when faced with the same positional questions. So far I particularly like the videos done by IM Shankland, IM Rench, IM Pruess and FM Lilov as for me they break the situation down into terms that I understand a little bit better than the other guys I have watched. I was also very impressed with the newer addition of Mark Ginsberg and I like his style of teaching.
Tactics Trainer is not one of my favourites as imo it doesn't simulate real play. In a real game of Chess (OTB) you usually have more time. I prefer to set-up a position on my board and work through it that way. The tactics trainer is good training for quick blitz games though.
Chess Mentor is also very good. It does as much as you could expect without actually having the Master there helping you. I'd like to see more videos tied directly to Chess Mentor courses, so for instance a video on a particular theme with a link directly to a mentor course by the same author on the same subject. For me this would help players put into practice what they have learned in the video.
A 
With so many great chess.com resources, what are your favorite / least favorite?
I'll go first:
1) Tactics Trainer--altough there are a few "whacked out" puzzles like a simple queen capture rated 1650. I think these are my favorite chess.com resource. I try to do about 20 a day. Keeps my tactics sharper. I hear a lot of crticism about TT, but I like it a lot. I just do the puzzles and ignore that timer, ranking, and puzzle strength.
2) Chess mentor--this is my favorite way to learn strategy on chess.com. It helped a lot with a couple of openings (KID and Sicilian) and general strategy (love Silman's lessons).
3) Videos--I know these must be very helpful. I'm not sure videos work well for me though. I find myself just passively watching. I find that I learn better by actually working out problems. I usually feel pretty dumb after the average video. The videos that analyzed amateur games worked best for me. I was able to relate to those better than GM games.
4) Computer Workout--seems important. It was very helpful to me for the less complicated situations like mating with the bishop pair, mating with a knight and a bishop, and certain basic rook and pawn endings. I get a little lost with the more complicated ones where there are many possible good moves, but only one best move.
5) Articles--I don't get a lot of these. Most of these seem beyond my understanding. I wish I was at a level where I understood such minor details about the game.
So, for any other players that felt like a chess retard around the 1600 mark, and found ways to improve your game on Chess.com, do tell your secrets!!