I organize double disc releases in their own folder under a parent folder for the entire release. It's cleaner when dealing with the files outside of the player and allows for a more standardized formatting of tags (track numbers) and file names. What I would love to see is album art being read from the parent folder as well and then displayed on the artist level with the other non-multidisc releases. The only way to make that happen as of now is to actually put a track in the parent folder with the art file and then Subsonic will read and display it but it's a messy solution. I won't do that. All my multidisc releases are sorted to the top and the art isn't displayed with the rest of the singledisc albums. =( I can't bring myself to just dump all tracks from all discs into a single folder either. I have some box sets that comprise 80 to 100+ tracks and several box sets have different art for each disc and I don't embed art into the files, instead choosing to do a single folder.jpg in the album folder. It's more manageable that way. If you need to change art you just change that one file and it's the most cross platform solution outside of embedded art, which I greatly dislike.
Sindre, please make Subsonic read the art file out of folders without tracks in them. Make it an optional thing if need be. I understand it could be messy for those who don't put in the time to keep an organized collection but I'm guessing most of those individuals don't care about this subject any way. For those that keep entire scan sets of covers, back and insert then make a standard for naming the art that one wants displayed. I use folder.jpg because that's also used by many other applications for cross platform support. WMP12 for instance uses the folder.jpg convention as well.