Game Promotion in site would be a great feature, something similar to what AdDuplex does. Basically, you get an impression for each person that views your game, then for an exchange ratio of maybe 8/10 (you get 8 ads for every 10 shown) you show a users custom ad somewhere on the page for their game. It's like a specialized in-site form of advertising. This could be used to replace the random game or as a "Featured Game" in the recommendations.
Gamer Streams. For the contest you showed Streaming, it would be nice if you could reintroduce that as a permanent feature so the developers could stream their progress. Alternatively, Gamers could sign up and stream themselves playing Game Jolt games. This serves as promotion for the Game Maker and as incentive for gamers as they can now earn money on Game Jolt for playing games.
Further API integration. Things like Sessions and Achievements could and should be integrated more heavily with the site. This creates a bigger form of community.
cmaspupra's Idea is another great idea, though possibly time consuming. Moderator's picks might be another option in which each Moderator can add games they like into a Queue which is cycled through (only if a new game exists) each day. That way you can continue to focus on making Game Jolt great and also have a great new game.
Allow developers to submit their games for "Peer Review" to other developers. This is basically a closed beta open to all developers on the site. This way they can test their game with a smaller player base and look for bugs with people that have experience looking for and fixing those kind of errors.
Game Settings. This is actually an extension of the Game Jolt API's Data Storage. Basically, I want you to add a specific key to each game (With Roaming Storage Enabled) that allows a player to save their custom settings and sync them across computers. This is similar to what I am attempting to do in my C# API. But could be done better if it was specifically integrated.
Improve Game Recommendations. More click throughs to meaningful links equals more downloads.
While some of these will be less effective than others, all of them (at least in my opinion) would make Game Jolt better.