Unfortunately, there is no 'ultimate iPod manager'… yet.

I got my iPod almost 2 years ago and I probably used iTunes for less than a day before I developed a distaste for it.  I didn't like the 'my way or the highway' attitude it had.  So I took the highway option and it's been a rather long journey since.

iTunes didn't recognise any changes I made to my MP3's outside of iTunes.  It had no idea if I moved an MP3 or even if I changed an ID3 tag.  iTunes could rip MP3's but it couldn't ensure glitches didn't occur due to scratched or dusty discs.  This was important to me when ripping thousands of songs.  I didn't need an iPod manager to do these things as I already had programs that did them wonderfully.  I only need an iPod manager to get the tracks onto my iPod and keep it in sync with my changes.

I wanted to try Anapod, but the trial version was functionally crippled.  So there was no way to find out if Anapod would meet my needs without purchasing it.  That really annoyed me.

I tried ephPod which works pretty well.  It can keep your iPod in sync with you locally stored MP3's and it does it well.  But development seems to have halted and support was never included for smart playlists.  Even if you created your smart playlist with iTunes, once you had uploaded tracks with ephPod they lost their 'smartness' — recent played tracks did would not appear in the 'Recently Played' playlist.

Despite the lack of smart playlists I stuck with ephPod until I signed up with last.fm which advertised YamiPod as an iPod manager that could submit tracks you had played from your iPod that you had listened to whilst on the move.  YamiPod couldn't create smart playlists, but unlike ephPod, it didn't stop them from working if you created them with iTunes.  But it seemed to conflict with other applications I used, causing slow response or freezing.  And it's syncing was extremely slow, cpu intensive, and would produce duplicates.

I also tried the iPod plugin that comes bundles with Winamp, but like ephPod, it stopped smart playlists from working and I couldn't find any documentation or support for it. 

I had tried ml_ipod plugin for Winamp many, many months ago and it didn't seem to offer anything over ephPod at the time, but trying it again now I've found it to be an almost perfect iPod manager.  It can synchronise changes from your MP3 collection to you iPod and visa versa, including playcounts, rating and played date.  It uses Winamps media library which, unlike iTunes, is smart enough to detect and recognise any changes you might make to your MP3 collection outside of Winamp.  It has limited support for creating smart playlists.  It doesn't offer the ability to create a 'most' or 'least' playlist, such as 'most frequently' played.  But this isn't really an issue as you can create these types of playlists with iTunes and it won't create any conflicts.

ml_ipod still has some bugs, but nothing I haven't been able to work around.  I can't confirm how well it works with modern iPods, but it's great for my 4G.  My only real issue is the lack of activity on the forum, making it difficult to find answers to some common issues.

UPDATE: I should also mention that whilst ml_ipod will not submit tracks played on your iPod to last.fm, you can still use YamiPod for this purpose.  I think you need to run it before you sync play counts in ml_ipod.  I should also mention that whilst the ml_ipod forum isn't very active, I have more recently received fantastic support from the developer with issues I've discovered.  The issue linked to above was fixed within a day.