I've really become tired of iTunes.
I started out sync'ing to my iPod using Amarok. It managed my collections well and even was able to perform transcoding on the fly, turning my FLAC and OGG collection into easily-digestible MP3 transmogrifications. However with my sixth-generation iPod I started noticing clipping artifacts and had problems with video cover art, so I decided to give iTunes proper a whirl.
First off, all my music is stored on a central file server downstairs. My upstairs LAN is connected to the downstairs LAN using a 10Mbs HPNA 2.0 bridge, so file transfers aren't exactly fast between the two. Still, with Amarok this wasn't an immense problem as I could transcode once during synchronization and just be done forever until I wanted to sync another album with the iPod. With iTunes however a choice few tracks (say 200-some out of 10,000) were always synchronized, so I was saddled with 30 minute synchronizations every time I plugged in the iPod. It was ridiculous.
On top of that the interface isn't exactly great. I'd like to list things by album and then by track as a tree-like hierarchy, which iTunes doesn't do very well. While browsing by artist was fine browsing by album was not, taking multiple-artist albums and littering them around. Plus album art was choppy at best; sometimes it would apply the album art, sometimes not.
I'm reverting back to Amarok now. Not only should synchronizations (especially podcast synchronizations) be more efficient, I now am not tied to the iPod as my music vehicle of choice. Should I decide to sync instead with a FAT32 thumb drive, or a smartphone, or a wax cylinder, it doesn't matter as long as I can mount it as a filesystem.
I still have transcoding problems... without a doubt; but now I know iTunes isn't a solution.