you can convert as long as you have a conversion tool. make sure if they are for iPod only use that you select using a QVGA resolution of 320x240 because otherwise it's pointless.

also note because of the decreased resolution text may not show up at all. subtitle tracks may first have to be rasterized to the video layer, though i'm not entirely sure how the ipod handles them or how to encode them onto a quicktime compatible AVC/ASP container.