I recently tried to find a good software to convert a bunch of videos to an iPad compatible format on OSX without buying some weird FFMPEG frontend.
Since it cost me some of my time, I thought sharing my results would be the right thing to do :)

First of all, the search for graphical OS X video encoders is horrible. There are a LOT of sites spamming the google search results and filtering them out is almost impossible. At first, I tried using handbrake. Handbrake does an really nice job when it comes to converting DVDs or single movie files, but it is not that great when it comes to batch converting 100 small video files.
The formerly commercial Visualhub and iSquint are available for free now, but only in their raw sourcecode form. Compiling them would probably also include compiling ffmpeg, x.264 and about a gazillion other libraries which is not something I was looking forward to just to convert a bunch of videos.
My final choice was Videomonkey. It seems to be a modified Visualhub (or as it is called now: "TranscoderRedux") that is in somewhat active development.
The latest binary release at the point of writing is version 0.8 and got released April 2010.
Here are some screenshots:
Videomonkey FormatsVideomonkey Thumbnail
While it doesn't have a proper iPad template, setting the preset to iPhone, selecting the "TV Screen" option, enabling H.264 and setting the quality slider to "WiFi" gave me quick encodes with acceptable quality.
If you feel adventerous, there are links to 64 bit builds of ffmpeg and iPad presets in videomonkey's forum on sourceforge.