Don't know whether this can help you further but someone posted these sort of Linux alternatives for iTunes:
Amarok (the only alternative which has actually most functions of iTunes and looks quite similar and provides iPod-support)
Yamipod (only to manage the iPod)
Rhythmbox (mainly to manage the iPod)
Or did I misunderstand your question?
some iPod touch devices are supported and others not
Extract from the posted link above:
iPod Touch and iPhone
Devices with Firmware 1.x
Jailbroken iPhones and iPod Touchs (models introduced in 2007 only) with firmware revisions not newer than 1.1.5 with ssh installed work if their /var/root/Media directory is mounted via fuse/sshfs and if they are added manually as a media device. Then you can copy music via Wi-Fi with libgpod 0.6.0 or newer.
There is a step by step howto on http://www.fredemmott.co.uk/blog_121
Recently, another method to access the iPod/iPhone filesystem, which does not require the device to be jailbroken, emerged: the FUSE filesystem iFuse allows to transfer data via USB. While the filesystem level access works for all iPhone and iPod touch models and firmware versions, the problem of computing a correct hash value, which is accepted by firmware revisions 2.0 and newer, is not yet solved and makes it impossible to transfer music to these devices.
Devices with Firmware 2.x
Using Amarok to transfer music to iPhone 3G and iPod Touch 2G (models introduced in 2008) and all other models of iPod Touch and iPhone that have been upgraded to firmware 2.x requires the phone to be jailbroken, you must edit the file /System/Library/Lockdown/Checkpoint.xml on the phone, finding the key DBVersion and changing its value from a 4 to a 2. Then follow the instructions as for firmware 1.x (sshfs or FUSE).
In addition to this some people appear to have (partial) support for iPod Touch under Linux using Songbird.
Amarok 2 will ship shortly with iPod Touch support. For now only Songbird can be used, but iPod-support is not stable yet: http://www.getsongbird.com/
Edit: you have to install this Songbird add-on: http://addons.songbirdnest.com/addon/12
Apparently the Touch is about the worst supported of all types of iPods in Linux, don't know why, but keep faith, it will only be a matter of time for things to get better