Since moving to an Apple iMac a few months ago, my new favorite video conversion tool is HandBrake. I still use ffmpeg, mencoder, and AtomicParsley as my batch-processing tools, but for queuing up multiple video files for conversion from AVI to MP4 format, I like using HandBrake (with its easy-to-use GUI). The version I have (64-bit for the Mac Snow Leopard OS X) runs very fast and produces excellent output. It also has numerous controls for adjusting the converted output video.
Note, that HandBrake is available for the Microsoft Windows OS, and I in fact used it a few times on my Windows 7 machine in the past. However, when I used my Zune HD I primarily converted my videos to WMV fomat which is something HandBrake didn’t do too well. So if you’re looking for a robust and fast video conversion tool for either the Mac or Windows machine, I recommend using the freeware Handbrake product and converting to MP4 format (for the Zune or iPod device).