Get those ditties offline! Use VLC Player to transfer your mp4, avi and mkv files from your desktop to your iPad. Connect your iPad, open up iPad within iTunes, select apps, scroll down to vlc app and add media.
Fun side note - when your not physically connected, you can grab files off of your Plex server through the vlc iPad app and download to device without having to purchase a Plex pass.
- not necessarily your question but I was stoked when this worked.
There are other nice apps out there such as nPlayer and Infuse which can access your video files from devices in your network which could be desktop/laptops and ofcourse also NAS devices so you can access video files and stream or download these to your iDevice and play them via those apps.
I haven't been using iTunes on desktop/laptops since years because I always hated that program because it's slow and never did what I wanted it to do (e.g. sync).