Just to pop in with my two cents worth, for uploading to YouTube, I was mostly just sending the compressed/rendered output from editors like Vegas or PowerDirector, but I too have gotten tired of the longer upload times and have started to pre-compress my videos before uploading. I generally switch between a few different utilities, depending on what I want to do or how deep I want to control the settings. For somewhat-'batch'-oriented converting, here are some of what I use:
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Handbrake is a good (and popular) free one, but you have to select each file one by one and set the quality you desire for each. For YouTube (not keeping for long-term archiving purposes), most people should be fine with just setting CRF=20 and letting'er rip, without changing anything else at all from the Defaults. Then, upload the now-smaller output. It is 'decent' quality and should be much smaller than a high-quality, large-size editor render output. If you are converting some videos for yourself to keep, you can delve into a lot more settings, too
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WinFF is an interface for the FFMPEG utility, which I started using back in Linux, but it has a program for Windows too, and it's free. My favourite thing about WinFF is that once you set your profile (which keeps your settings, compression quality, etc), then you can BATCH select a whole bunch of files to convert at once and just let'er rip. Set it once, then forget it. The only drawback is that it can't use hardware rendering/compression, but that means it will end up with somewhat better quality anyway
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Nero Recode is much better these days than their older version, with the same ability to choose a whole batch of files at once and just tell it to 'go', after you set your profile/settings one time. It can use hardware rendering and you can easily set the Deblocking and other advanced H.264/AVC options. I bought the suite from Nero a couple years ago and still run it once in a while
» CyberLink's
MediaEspresso came free with my recent purchase of PowerDirector, and I have only started using it a bit. It seems to be easy to use, batch select in one shot and pick a profile (PS3, PSP, and so on) and it can use hardware rendering/compression and even do a little noise reduction/filtering, all with one input from the user. It seems fast, but the quality seems to be a little behind the other programs at the same rendering options/settings. I might bring that up with CyberLink
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Bandiconvert doesn't exist yet, but I am hoping and dreaming at night about a program that can let you make a setting for compression and quality, then select a whole batch of files at once and tell it to compress them all in one step - I submitted this idea of mine to Bandisoft and I'm rooting for them to make it happen!
Hopefully that gives you more ideas on programs to try