I'll give my 2 cents

* Allow edit comments on wallpapers (or allowing to delete and than comment again). Currently if you delete you cannot comment again
* Allow comments on scans, sometimes you cant to praise a vector, ask for another version or point the fact there is another version of it and you must do that thru PM, and sometimes it's nice to see people sharing toughts on a scan.
* Allow fav without comment. Would prevent people doing useless comments just to add favs
* Better BB code editor on top of posting area would be nice =/
* I know the answer is no but since you asked: smileys? >.>
* Special area for wallpapers in progress instead of a Forum (SessionZero)
* Allow one to reply to individual messages when commenting a wallpaper (like deviart)
* Allow to add a comment when reporting something wrong with scan/paper. Some times I want to report something that is not listed (instance: porn) and I can't, have to PM a mod
* Make this site more inter-browser friendly. It really is slow on IE
* Allow multiple categories for a wallpaper
* Paging at category on scan/wall. That page tents to grow as more anime is released, it's already huge xD~
* Allow people to delete posts on their guestbooks, or at least a report function to it
* Allow searching for resolutions (##x##) or aspect (wide, 4:3, 5:4) on wallpapers
* Keep outgoing PM's so people can keep track of what they sent (might be auto-pruned after a time perhaps)
* Prevent visits/download horing on wallpapers to try and manipulate rank (log IP? dunno ... or change the current rank math)
* Give paper awards (like, 5 papers) for a correct report, to incentive people to report rips/dups etc... I see a lot of them but quite frankly I fell like tired of even trying to search for the dup just to report it (I know they are dups, but I don't want to locate them for instance) xD~ yeah I'm lazy, but that's the same philosophy of giving papers for people who participate right? =p
* Allow usage of shoutbox as search (if shout matches an anime title, just throw the user to the category index XD)
edit
* Allow alternative upload version so people can upload wide and 4:3, or the same aspect but with different themes
edit 2
* Make it so people receive only ONE notification for comments on a given wall or scan. So you don't log in to see you have 20 notifications for the same thing ><; in short: would only add a new notification if there is none for that scan/wall (you must delete the notification if you want to be informed of new postings)

that's just 2 cents >.>