If the files are DivX/XviD and they are to be played on a standalone player, the .sup files can be converted to sub/idx format using 'Subtitle Creator' and the sub stream added using the likes of 'AVIaddXsubs'.
These Xsubs are not viewable on the PC with a media player, but can be switched on using the remote on a standalone DivX player.
Another alternative is to add permanent, always on subs, using VirtualDub and the VOBSub filter.
The Sub/IDX (VOBsub) format is a bitmap format so there's no problem there.
I don't know much about Ipod- I thought the subs had to be burn in (permanent).
I believe 'AVIDemux' can either convert to Ipod format or embed the subs using it's 'Filter' settings..
One way, try 'AVIDemux'.
Load the file.
Click Auto => IPOD => OK
On the left sidebar of the main window, under Video, choose 'Filters'.
Select 'Subtitles' and 'VOB Sub'.
Load the IDX file and use preview to see the result.
Save the file by giving it a new name plus extension, eg new.mp4
when I load the mp4 file, the program crashes. then, when i run the program again, it gives me a message that says "I have detected a crash file. Do you want to load it? (It will be deleted in all cases, you should save it if you want to keep it)", and the options "load it" and "cancel", but whatever i do, when i load the subtitle files, the program crashes again