I am an Ubuntu user at home, and I have of course iPad but also an iPhone. The iPhone is currently well supported under Ubuntu for music/videos/photos management. For the iPad, that is another story (at least until the support is available).
So how to put some media on the iPad if you are using Ubuntu? Here is what I do...
I have setup a PC running Ubuntu and the upnp mediatomb server. It is quite easy to install and configure using the package manager. Then, on the iPad, I use a upnp client, Fusion Stream, to connect to my server. Actually, you don't really need a dedicated server as you can simply use your laptop to host your medias...
The great thing is that your media will be organized via the mediatomb server, and Fusion Stream gives you the possibility to download a local copy of the media on your iPad.
Since I have 2 iOS devices, I wanted to have a single source of media to avoid keeping my movies on each device. So having them in my media server and watching them in streaming over wifi makes it easy to manage the movies.
So, once everything is setup, I just use Fusion Stream to connect to my media server and watch my movies when I want to. And having a tv out cable, I can watch those movies on my tv also. Oh, yeah, since Fusion Stream does not support tv out, I simply use safari on the web UI of mediatomb to stream the movie to my tv. Works really well.
The fun thing about this setup is I do not have to sync my iOS devices at all. As everything is done on the computer.
For video transcoding, I use FFmpeg (compiled from the repo sources). But there are a lot of software that can do this....
A quick how to:
1- install mediatomb
2- install Fusion Stream in iPad
3- configure mediatomb from the web interface to add media folders
4- connect on server using Fusion Stream and browse/download/stream your media files
Have a once day!