At first I hated iTunes, but I just needed to change some habits such as only adding the files I would sync to my iPhone; the thing I hated the most was having 2 copies of songs when getting an WMA archive converted to AAC encoder (M4A files).
Then, I decided to just import my whole music collection to iTunes, following these steps:
1- Changed iTunes importing options to MP3 (@ 192 kbps)
2- Added all WMA albums, so I got an MP3 version of all of them
3- Deleted all the WMA albums from my collection
4- Moved the albums from the iTunes' Music folder to the corresponding folders in My Music (where the WMA albums used to be)
5- Searched for the newly converted albums in iTunes and deleted them, as they are not a copy of the music but a reference to the actual MP3 versions
6- Re-added the albums, now being MP3
If you don't care about having the albums inside each singer/group folder, you can just avoid steps 4 through 6.
It may seem a lot of work (I have 77GB of music) but it is totally worth it, as now I can play my whole music from iTunes and sync whatever I want. iTunes also helps me to clean my collection by identifying duplicates and leting me select all the songs from an album and making changes such as changing the Genre and adding the album artwork (I'm using
Album Art Exchange - High Quality Album Art / CD Cover Art: Home to look for 600x600 artworks).
I hope some of my ideas help...