I use the following two options:-
a) Convert with Handbrake (avi, mkv etc to m4v), drag files into iTunes and sync iPad.
b) VLC installed on iPad, within iTunes add files (avi, mkv) to VLC documents.
Normally follow the first option but the second is used if I need to throw something on last minute and don't have time to convert first.
This. and as said if you have a lot of avi's and simply want to transfer and not encode then install VLC and under iTunes add 'files' to the VLC app.