I would not attempt to use Subsonic for video. As great as it is for music, it still has some bugs on the video front last time I checked with was a few months ago.
I would recommend Air Video for the iPad as it has worked flawlessly for me since day one, uses Bonjur on the local network and will transcode over the network in realtime which is crucial if you download a lot of movies and don't want to have to convert stuff into a special format.
I have played .flv .avi and .mpeg flawlessly with Air Video from my iMac which is connected via ethernet.
You can also use Air Video over 3G if you are familiar with port forwarding.