I have 2 questions here
Is there a program for Linux that can manage a sony md device, like Gnomad does for the Creative products

And also is there a program that can write flash cartridges for a game boy advance
like Littlewriter for Windows

Try searching google. That would be a better place to look. As far as I know there isn't a Mini disc program (I assume its for sony's NetMD range?) because the protocols are strictly proprietry as well as the codec that the NetMD uses (I could be wrong on the last part). You should still be able to record using a line in cable from the computer to the MD if you don't mind waiting.

The other program seems relatively specialised and possibly illegal so probably no one will help you any with that. If you really want something for that purpose google is the only way you are going to find it.

Hope that helps

Alex