1. Introduction
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Ubuntu can be configured to sync music and photos using a USB cable. This page describes how to sync music and photos.
2. Syncing Music
2.1. iFuse
iFuse is a FUSE-based access method for the iPod Touch and iPhone, making them appear like normal hard disks. It has been in the Universe repository since Ubuntu 11.04 (Natty Narwhal), or can be downloaded from the developer's website, here.
To sync music with a jailbroken 2.2.1 iPod Touch, install iFuse from the project's repository, then plug in your iPod touch. HAL should pick it up and GTKpod will see the device. As long as you have changed the value of the key 'DBVersion' in /System/Library/Lockdown/Checkpoint.xml (make a backup first!) to 2, music will sync and the database of the device will be updated. After restarting the Music application on the device, you should see the new tracks. This method does work.
One annoyance is that while HAL will automount the device for you and place it on your desktop, you cannot unmount it manually by the usual methods (umount, or right click and 'Unmount device') because the FUSE mount was created by the hald/system user and not your username. However, if one takes care to right click on the device in GTKpod and select 'Eject iPod' before disconnection, harm to the filesystem may be avoided.
2.2. usbmuxd
usbmuxd is the successor to iTunnel. Both of these softwares provide connectivity over USB for iPhones. usbmuxd has been in the main repository since Ubuntu 11.04 (Natty Narwhal) or can be downloaded from the developer's website, here.
2.3. iTunnel
This section applies to a redundant piece of software. New users should use usbmuxd.
To install and configure iTunnel:
Go to the iTunnel project homepage and download the iTunnel program for Linux. It includes a binary or compile your own.
Start the Binary in a Terminal/Xterm and create the Tunnel on a self chosen port with ./itunnel 7777.
Mount the ipod's file system with sshfs -p 7777 root@localhost:/var/mobile/Media /media/ipod.
Set up the FirewireGUID as described in the Firmware 1.x Guide.
Start your Program for transferring MP3s ( amarok etc. ) and point it to /media/ipod. You should be able to transfer Music to the device.
2.4. Speed
iTunnel gives me about 400kb/sec iFuse gives me about 250kb/sec WLan gives me about 10 - 800kb/sec, WLan crowded places give less 
It is a good idea to create a Ad-hoc WLan and connect directly your iPod to you PC. I take speed up to 1,5MB/sec.
3. Copying photos to the iPhone or iPod Touch
Photos can be copied into the Media/DCIM directory in the mobile account. They need to follow the directory and image numbering conventions used by the iPhone/iPod. Multiple image formats are allowed, but they should have a thumbnail (.THM) file which is a 55x55 pixel JPG file.
There is a command-line script that can copy images to the iPod Touch or iPhone using ipod-convenience or scp available here.
Note that it is free to use and source available, but not technically open source.
3.1. Alternative method using a webserver (3.x)
You can use a webserver set up, accessible either via a local IP over wifi or a hosted server to transfer images to your iTouch or iPhone. Transfer the image to the webserver (/var/www/photo.jpeg), and then go to your IP in the web browser followed by the relative path and filename of the image (192.168.2.4/photo.jpeg), then hold your finger on the image until options appear. Click "Save Image" and it will be available in your photo browser for using as a wallpaper or whatever.