I realize this may not be the most popular feature request due to the non-zero possibility of the re-encode not playing correctly. However due to the solid experiences I have had with the trancoding system in Plex, I would love the following feature:
Take the original file and reencode it using H264 High Profile (with Web Optimized options enabled) with additional audio tracks 1) AAC and 2) original AC3/DTS if available. I use a low power (AMD E350 based) server and can serve files encoded using handbrake with the aforementioned settings. I have difficultly serving non reencoded files due to the low processor power of my server.
During my reencoding, I also discovered that the resulting files are about 32% smaller on average than the original files. (Which was a nice bonus.)
I would love an option that would go through the library and verify that each media file has the previously mentioned formatting.