Yeah, I've been using the free Videora iPod Converter as well:
http://www.videora.com/en-us/Converter/iPod/It's working quite well -- small, free, stable, has a variety of options, and does the job. And it's built specifically for this task, so it performs in a way that only a speciality program can (meaning, regrettably, it can't do anything else, but, thankfully, it doesn't try to do anything else). Since the itunes digital rights management stuff doesn't come into play with files that you create/convert on your own, MC is able to upload them without a problem, even if you don't have itunes installed, etc.
Of course, Videora's got so many options that it can be a little difficult to figure out what settings and formats are best -- I visited a few websites on the topic, and everyone seems to have a different opinion, none of which correspond with the Videora defaults. So you've gotta play around with it for a while to see what's best for you.
Also, you need to decide on the quality vs. size issue in so far as the ipod doesn't need a really high-quality file (since it's such a small screen), so you're really better off going with a lower-quality file so the file size is smaller (so you can fit more videos on your ipod). But this means that you'll want to keep the higher-rez version of the movie/video on your PC (in case you ever want to watch it on your monitor or a TV, etc.)... which could be annoying if you don't want to waste room on your hard-drive keeping two of each file (one high quality for PC playback and one low quality for ipod playback). If you'd prefer to only keep one copy of each of your films/shows, then you'll want to convert everything to high quality and erase your old files, but that means the files will take up a ton of space on your ipod. So, again, you'll want to play around with whatever converter program you're using until you find a size-to-quality ratio that you're comfortable with.
The other problem is that converting video does take a while. Even converting just a 4-minute music video took ... well, I'm not sure how long, but it felt like forever... and converting longer shows took, as you might expect, much longer. And then uploading video files onto the ipod isn't exactly super-fast either.... all-in-all, it makes me wonder if it's all worth the trouble, in terms of converting and uploading all my old videos, films, and TV shows, just so I can watch them on the little screen.
Of course, now that the video ipod is out there, people will be more likely to rip DVDs and distribute music videos and such in an ipod-video compatible format (you're already seeing that kind of thing among bittorrent users) so things will only get easier. It was a rather brilliant (if nasty) move by Apple to only allow a couple of specific (Apply-centric) file types to be used on the Video ipod, since it's going to popularize these formats in a wild, crazy way.... Much like the way Apple shot so many music-file formats in the foot to begin with (thank god iPod accepts MP3's, anyway).