Full Widescreen support because, from my young perspective, everything seems to be moving that way, computers and TVs alike. Please make support for all kinds of resolutions. To really keep things looking uncluttered, make them advanced options.
Personally, I don't like the way the controller pluggin looks. N-Rage looks terrible, but a simple picture and such for Jabo's pluggin would really make it look tons better and LOTS less confusing to people using it the first time.
Multiple button support and such for key mapping. I don't need a reminder from the pluggin telling me I mapped the same key twice, even worse, not letting me do so. It makes life hard, harder than it already is.
Anything that can be opened and browsed through WinRAR would be helpful in the rom selector. Ex, WinRAR opens .7z. The same .7z everyone wants in PJ64. The way that browser is set up looks real easy to use. Jnes has things looking really good, but gets pretty annoying when you have many files in one folder. Alphabetically organizing files into folders (A, B, C folders) helps for me, but if PJ64 has a unique, original approach to this, Kudos to you.
This one may be controversial, but Hi-Res textures support. If anything, at least as an advanced option. I understand the point is more towards emulation and not improvement, but then why add savestate?
Video Clip support. There's enough justification for that.
Skins was a great idea mentioned by someone earlier. You could improve the GUI however you'd like, but making some specification for skins the way Windows Media Player and Winamp does would let others customize PJ64 to match their desktops. Without some kind of customization there, you'd either have to make something that looks plain to match everyone's desktop, or really cool but only look good for some people. Shows like "Pimp My Ride" did extreemly well in their first season for a reason.
I don't know if this is a good idea or not, but transparency would be a real modern enhancement. Keep the release looking cool until 1.8 shows up

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**More options in the sound pluggin to play around with, unless you perfect it of couse. Things like sound quality adjustment, or a PITCH BENDER would set you guys apart for sure. Or how about playing mp3s or certain media formats in place of game songs like the Sega CD did? Eh?
I'll be happy with whatever comes out.
I'll think of better stuff later.