ok so i used a youtube downloader to get some mp4s on my laptop, then transferred them to my desktop using a usb stick.
now when i try to put them on my ipod, they play on itunes but wont go onto my ipod.
when i look at the files somewhere else, the thumbnails are orange cones.
does this have anything to do with it?
how can i fix this?

The icons are orange cones because VLC is the default application that will play them. This has nothing to do with iTunes. iTunes will play some videos on your computer that won’t work on your iPod, try http://mirovideoconverter.com/ or http://handbrake.fr/ to convert your videos to be compatible with your specific iPod and then add them to iTunes again, it should sync to the iPod fine after that.
Right click on the mp4 file -> Select Open With -> Choose the Default program