If you are using Windows then there are a few worth looking at and trying. In my experience, the best apps are those that are front-ends to some low-level encoder like ffmpeg or mencoder. Some of the other apps are much more user friendly, but sometimes the end result is not as good, and you don't have as much control over the encoding process to try to improve it.
I used to use avidemux for most of my vids. With a bit of work, once you have the default settings you want to use, you can turn them into a script which can be saved and turned into a menu option, just choose it next time and all the same settings are applied. You can also create a list of vids to work on and let it run through that list.
It's also good for encoding just part of the input video. I often used to do one continuous recording of a channel, then use avidemux to output separate files for each girls session, and it will even split the recordings into smaller pieces for easier posting on your file hosting site if required.
Recently I am favouring MeGUI instead. It doesn't always work with some videos, but when it does it seems to produce a slightly better result than avidemux, and I don't get as many syncing issues with sound. I use the one-click encoding option and add vids to the job queue for it to work on in batch.
I used the most recent version a while back and had a major issue with it only outputting in mkv format, I just couldn't switch it for some reason, but I had an older version setup just how I wanted it, with a default output of xvid/avi, and I updated that, and it still works fine, so maybe it was me, maybe not, I don't know.
Another worthy mention is SUPER from
http://www.erightsoft.com It's not the most elegant looking app, nor the most user friendly, but once you get used to it, it's actually pretty good at doing its thing. Like MeGUI, it doesn't always work if there is some slight issue with the input video file, but when it works it works pretty well, and not as slow as some others. It uses both ffmpeg and mencoder, and sometimes one will do a better job than the other, and you can also use directshow drivers or not which may improve the output.
So that ones in the dumps. Hopefully your recommendations will be better.
I'l try it again later this week with larger files and hope to avoid any sync issues. I only ever get audio issues with Elite anyway and thankfully there are a few members who take care of those streams already.