Best Converter for iPod

So I got me an iPod. (I got a job during the summer and bought it.) It's a Classic with 160 gigabytes, so naturally I want to abuse this large portable storage capacity as much as I can. So it's time to upload some of my favorite videos to it. Anime and various movies and stuff on my computer. (Gunslinger Girl is going on there first. I just found an English dub torrent.)

NOW, what I need, since most video formats aren't compatible with iPod, is something that MAKES these videos compatible. I need a good iPod Classic video converter. Something that converts videos to whatever format(s) iPod Classic can read.

Unfortunately, the last time I tried something like this the videos converted alright, but when I played them on my iPod they caused the thing to restart every time I tried to pause in the middle of the video or any song, or fast forward. It's a glitch that went away as soon as I took off the videos. (rmvb Naruto episodes converted to an iPod Video-compatible format) so I need a converter that can convert videos in just the right way so that this glitch won't happen with my iPod Classic.

Preferably, I'd like to to be able to convert flash video as well, because I've been using realplayer to help me snatch my favorite videos lately.

Any software suggestions? Obviously money is no object (because I'll just pirate it.)

It would really help if you actually told us what you used, and what format you started with, and went to, but what the hell:
http://www.google.com/search?q=ipod+video+converter

Oh, look at that. Videora. The program I used to do this exact thing on my old ipods. And it's free!
Thanks, Google.

You should not have got a crippled, restricted, overpriced iPod.

But now that you have one, use MediaCoder. It has profiles for various ipod formats.

@arlen: I appreciate the help, and the coder looks good, but whenever I get to the part where it's time to confirm the file to be converted, I get over 9000 "Internet Explorer Script Errors" and none of them let me click out of them because they're all being lagged by the next ones. Is there a way to change this program so it runs with a superior browser, like Firefox?

@Roph: I'm trying out your suggestion now as well. I love your new avatar btw.

Alright, using MediaCoder, what options should I choose when converting the video? Like format? I'm using a standard 6th gen iPod Classic 160 gigabyte device. I got it yesterday.

One more issue: When I used mediaconverter, the file refused to play. It said "cannot start playback" and couldn't be added to the iTunes video list either.

EDIT: After using arlen's suggestion again, I found that the Script Errors happen a lot less if I click slowly.