I've been using a WDTV Live since last year (since Goodbye put me on to them over on MacTalk). I've been investigating alternatives recently since WDTVs all over the world have suddenly started going on the fritz (cause of which still uncertain at time of writing).
The thing that I've found frustrating is the lack of support for deeply nested folders. The AppleTV is the worst. But Plex also seems very limited - can do folder for the program, subfolder for the season, and then the names of each episode (no matter what their title, they're just listed as "episode 1" etc), and that's it. XBMC's similar, I think?
It's just so limiting. Back in the days of Front Row (ah, those were the days...) I could have a folder called Documentaries, then Time Team, then Season, then Episode (with a title that's more useful than "Episode 7"). All very logical, easy to find things. Sure, Plex and XBMC and others give me pretty pictures, but they're a poor substitute for actual usability. WDTV was about the only thing out there that supported it.
Thankfully, it looks like a firmware rollback fixes up the WDTV so I'm back to that now. Hopefully by the time that finally kicks the bucket there will be something that's both pretty and supports simple organisational functions.