On a related subject, are there any pdf-splitting (I.E. individual pages) free programs for linux?
Look up pdftk. It's based on the Java pdf library iText. So you could write a program using this library to do it also. The clunkiest option is using ghostscript. In environments that don't allow 3rd party tools (i.e. my work) I've had to make a script which splits the pdf using ghostscript. It's not pretty, but it'd doable.
Before I go and spend time programming my own, is anyone aware of a free program that can take images from a score (say from an extracted score pdf on this site), and attempt to split it into the different parts?
This isn't an easy problem. Many scores omit parts in systems where they just rest. The same part will jump around from system to system. I've also seen horn parts switch the pairing. For one system it will be I+II, III+IV then for the next it will be I, II+III+IV. Many times full scores omit the short instrument names at the beginning of the system. The instruments are determined from context.
I don't think there are any programs out there currently which try to solve this problem. I say go for it. Let us know if you come up with anything. Even if the input was the score and a list of staves to pick out of each system it would still be immensely easier than using an image editor.