I need help putting you tube stuff on my iPod.?

Alright from youtube I downloaded flv file. Now for iPod Video. I converted the flv file to MPEG4 but it gave me a Reference Memory sys error it said you still want to continue I clicked yes and then the file was really unstable and only partially played on iTunes. Then I decided that .mov files would work. I converted using converted to .mov and iTunes played it fine! But not my iPod. I think .mov might not be playable in iPod. Also I am not really rich so if its my converter thats the problem can someone tell me a good FREE converter. My current one is free because it places its logo in the middle of the video but I dont care about that as long as I can play on my iPod. Please anyone help me.