Miro Video Converter

Miro Video Converter is a FREE (and Open Source) transcoding app. So far it looks good for its intended purpose.

Here's a list of it's capabilities so far:

Convert to MP4 Video
Convert AVI to MP4
Convert H264 to MP4
Convert MOV to MP4
Convert WMV to MP4
Convert XVID to MP4
Convert Theora to MP4
Convert MKV to MP4
Convert FLV to MP4

Add that it'll also transcode to Ogg Theora (video) and it's a pretty handy app.

Permute

Permute (NOT a free app) could be part of an alternative to the much missed VisualHub. It has a good selection of presets and you can modify them as well. It's clearly not for professionals who need more fine-grained controls or non-consumer formats but for quick conversion of things to xBox or iPhone and the like it could be handy.

I haven't done extensive testing with it but if you're looking for something to fill in the hole left by VisualHub this could be a good start.