1) Open Media Library - Another movie interface for Media Center that supports transcoding to extenders. It's free and under development. It appears to use a different transcoder than transcode 360 so those of you with transcoding issues might want to check it out.
2) PlayOn - PlayOn lets you watch Netflix, Hulu, CBS, YouTube, CNN, ESPN and more on your TV (using extenders). PlayOn supports Xbox 360, PS3, Wii, and I assume other extenders like Linksys. PlayOn has a 14-day free trial. The product costs 39.99.
3) vmcPlayIt - Let's you use PlayOn on your Media Center. I was looking for something like this so I could watch Hulu and such without having to use the extender. The developer takes donations.
4) Super - a GUI for mencoder and ffmpeg that is very tweakable and has preset profiles too. Free, but donations are accepted.
5) VideoRedo - Want to quickly turn your ripped .vob files into an .mpg or .dvrms file (other filetypes are spported too). This tool will merge the .vobs and fix the time indexing and finish a movie in about 5 minutes. It does not re-encode. I'm not really doing the product justice in my description. For example, you can use it to remove commericals from a recording. Free trial is available.