I found a handy little tool called mkvmerge. On Ubuntu and derivatives it's in a package called mkvtoolnix.
It's handy for when you need to split an mkv file up to get it onto a FAT32 filesytem such as on an iPod.
You can specify when you want the split to occur, or after how many gigs or whatever. This is how I used it to split a file roughly in half (after 3 GB).
mkvmerge -o output.mkv --split size:3g input.mkv
The tool works suprisingly fast and gives you two mkv files, which can then be transferred (albeit slowly on my system) to the storage device.