Well, I have always thought a few modifications would be cool:
1. Perhaps you can make a user-nominated section on the front page. Not only do we vote to determine the overall score of a NG submission, but maybe we could also flag a movie/game for a front page nomination. I've seen a lot of great NG posts that haven't truly received the exposure they deserve. Have the server tally up the nominations at the end of the day and poof, there you go. Call it the NG Users Award or something.
2. More control over the Alpha's page. I think the Alphas Page has more potential than people think. Let us edit our Alpha page by adding updates, answering user questions/suggestions, polling what content users would like to see in the final piece (etc.). What would be sweet would be to see a kickass game/movie on the front page, discover that it has listing in NG Alphas, and have the oppurtunity to see how it was made and who influenced its creation. I have a blog that I use to show how my game, Master Lao VS the IRS, is coming along (http://www.mondomaniatrics.com/blog/masterlao). This is sort of an example that I'm talking about. Also, giving us the ability to delete an Alpha page would be good. Sometimes, projects just end up souring. There's no reason to keep people's hopes up for a dead feature. Hell, I've been waiting for Pico 2 since forever ;P.
3. More attention to flash developers. NG is frequented by thousands of talented artists and programmers every day. Why not add some forums that they can better relate to? An artist's corner to showcase talent (already mentioned earlier I think), advanced Actionscript for gaming, the Animator's corner (for featuring frame by frame showcases or how to's), backend programming, etc. NG is primarily used for displaying final projects. I'd like to see NG become more of a community where people come come to learn. Besides, the Flashkit forums are drying up fast.
4. It was a great idea in the past, but I don't know why you haven't gone through with it: An NG user account that we pay for. Everyone is entitled to a free Newgrounds. But, god damnit, if it takes paying two bucks a month for a special membership to keep the porn ads off of my machine at work then so be it. If you keep the cost low, the amount of people who enlist should outweigh the revenue you earn on the porn. Don't get me wrong, I love a little hentai now and then, but having the boss walk in on those bastard ads makes it too risky to watch NG at the office.
5. It'd be nice if I could be notified by email when people respond to my posts at the NG BBS.
6. This may be too much, but could you place a user preference in the profile to only view graphic ads? I have noticed that the flash ads can diminish or slow the playback on some movies.
7. This may sound pretentious, but it would be sweet to have an NG-elite section. This section is devoted to and can only be accessible by the top animators and game designers on NG. Only those who've scored a high average on all of their submissions; racked up a quota of daily trophies, exceeded a certain experience point level (9+) could view the site. Even if it's just a message board or a chat section. I'm sick of wading through hundreds of submissions/questions/comments made by noobs. God knows we're here for them, but sometimes I feel like kickin' it with the pros.
8. Purely for my own interests: Set up a notification system to let users know that they're about to watch a stick flick. I'm sorry, but I just can't STAND stick figure movies. Knowing about it before hand would really save some time on my end. Then again, some people LOVE stick flicks, so knowing that the movie/game they're about to view would get them even more excited.
That's about it. Wow, this post is long. Hope this inspires some new ideas. But please finish "Pico 2" and "Dad and Me" before getting side tracked by anything else.
Keep up the fantastic work!