Media Juxebox is a wonderful product. As an owner of a PC and a Mac, Media Jukebox is by far the best mp3 player on the PC, the only comparable product in terms of features and usability is Apple's iTunes.
Note: I use Media Juke box with skins disabled, so my comments may only apply for this interface. I have not looked at MJ 9 Beta, so some features suggested here may be included in version 9.
1. My main GUI complaint is the 'playing now' view, -- it is very confusing. I would much rather the view stays in the currently playing category or playlist while playing. I would rather shuffle-play be performed by jumping randomly, rather then re-ordering the tacks into a 'playing now' view. For instance, I often want to reorder a playlist while listening, but once I start playing I jump into the "playing now" view, often without realizing it. I start to re-order the current view instead of the playlist.
2. Snap Pallets
A. Split the (A) Library, (B) Playlist and (C) Hardware into 3 separate pallets that can float or snap into the sides. Many windows application use this interface, such as Altova's XML SPY.
B. Snap-able floating play bar.
3. Rename and reorganize music files based on rules.
4. Update all tags and convert to IDv2
5. MPEG4 Playback & Encode plug-in (I'd pay an extra $10 to create ACC files)
6. Normalize entire library - does not re-encode files, but sets a user-adjustable volume for each track
7. An equalizer setting for each track
8. A more advance organization tool that allows for sorting by composer, and multiple genres, such as Classical, Baroque