I've been put off by the alternatives as they're still not what I want (i.e. most of them are still "music manager" apps with skinned UIs etc.**) and it's uncertain whether they'll work with hardware/firmware upgrades (Apple have a habit of breaking compatibility on purpose, going as far as encrypting the database format in firmware updates) and whether they'll support all the features (e.g. gapless, videos, games, podcasts...*)
I did use a very lightweight tool when I first got an iPod. It just showed a tree of files that you ticked on or off and would then sync them. That stopped working and wasn't updated for newer models/firmware.
Anapod Explorer looks/looked like it might be nice since it integrates with Explorer and provides a UI that is close to copying files to a HDD... Unfortunately, the demo version is quite restricted so I was put off installing it as I didn't think I'd be able to test it fully. I wrote, twice, to the people who make it to ask if it supported the iTunes database fields required for gapless playback (exact length tags) but they didn't reply with even a "we're not sure."
(*I don't use videos much but it's nice for a couple of TV episodes if I go on a long train journey. Don't use games on my iPod anymore after Apple screwed 5th gen iPod owners by telling us we had to re-buy our games at 100% cost to get the v1.1 updated versions that worked on the 6th gen iPod. I decided not to buy any iPod games, old or new, ever again as a result. I used to download a lot of podcasts but found I never listened to them... So gapless is the main thing, I guess. But, as crap as iTunes is, the alternatives would have to be massively better for me to switch to them and, from what I've seen, they're not.)
**EDIT: The UIs of some of the ones in the list you posted look okay, though.
I can safely say that the latest version of Notes is just as bad as previous version, it just uses more colours.
Thank you for confirming my suspicions that Notes hasn't changed!