This is exactly why I've held onto all my CDs, and why I continue to buy the majority of my music in a physical format. I once had Apple ... iTunes match? iCloud? I can't even remember what it was called ... decide that an Eminem album I had was too racy and serve me a censored, unlistenable version instead. And the complexity involved in keeping any kind of sizeable music library in check using iTunes is overwhelming. I have two apple ids, some music on an external hard drive, some on an internal hard drive, some subset/superset/overlapping set of which is 'somewhere' in the cloud; it's a nightmare. Is there a sensible alternative to iTunes that will a) not do anything with 'the cloud' b) sync to my iPod?
MediaMonkey and Fidelia are the two products that seem to be tossed around most frequently as iTunes alternatives, and which seem to be reasonably close to feature-parity (at least, as music players; they obviously don't do all the garbage that Apple has stuffed into iTunes related to the iPhone). If you want to basically get back to what iTunes was originally ("rip, mix, burn" plus a good music player and organizer), those are probably the best bets.
Personally, I've been slowly moving to having my main music collection on a home server, and then distributing it out to clients via Plex. I'm not 100% pleased with the web interface compared to iTunes' thick-client interface, but as iTunes' UI has gotten worse over time and Plex's has gotten better, they're starting to approach each other in terms of usability.
The main complaint I have with Plex right now is that there's not an option to specify the quality of the streamed music. It will do realtime transcoding (so you can store lossless CD rips on the server), but the destination format is hardcoded based on the client (I think web clients get 256 kb/s MP3, Android gets something else, etc.). There's an open feature request to let the user select it as a preference, and allow different codec/bitrate combinations based on whether the client is on the LAN, on WAN, or on mobile.
Plex is, IMO, the best game in town for approximating the functionality of a proprietary ecosystem (play all your stuff on all your devices anywhere) but without the lock-in. You do need to be a reasonably intelligent person to set it up, though.
EDIT: It's been brought to my attention that MediaMonkey no longer works on recent versions of Mac OS X, but that Swinsian (http://swinsian.com/) is the new hotness anyway. Can't vouch for it, but it looks good.
