I would like a boot partition for Win98, a data partition (could this be accessed by Windows, Linux and WinUAE if it is using the PC file format, how about FAT16, FAT32?), and a Linux boot partition.
I'm assuming you want to be able to get maximum usage from all of your OS's/Emulators - so you'll need to go with a filesystem that is a 'common demoninator' -- I'm going to suggest FAT32, as Windows needs it, and Linux can read it and use it.
Many people have suggested using hardfiles for WinUAE - As I use UAE on Linux, I'd say go with their suggestion.
Under Linux there's a bunch of 'dirty tricks' I can do by NOT using Hardfiles - but that's another kettle of fish.
As for Dual Booting - You'll want to install Windows first - it will want the first partition, and will more than likely set the MBR on your harddrive (someone correct me if I'm wrong on this)
Installing Linux second will let you put Lilo in place and you'll be able to boot Linux from wherever you put it.
Also, does it make any difference if I have a separate swap partition, or can I have this as part of the Linux partition?
Linux swap is its own partition.
Siggy.