The best way to do it is under OS X (10.4.2 in my case) using diskutil. My drive is 160GB, so I did a 100GB FAT32 partition and a ~60GB HFS+ partition. It’s as easy as:

diskutil partitionDisk disk2 2 MBRFormat MS-DOS FAT_VOL 100G HFS+ MAC_VOL 60G

Diskutil will figure out the change on the 60GB partition if you go over the free amount (it came to something like 55G).

You need the MBRFormat parameter if you want Windows to be able to read the FAT32 partition. If in doubt check the man page.

Using either disk under Linux 2.6.x is as easy as:

mount -t vfat /dev/sda1 /mnt/exthd1/
mount -t hfsplus /dev/sda2 /mnt/exthd2/

You need the vfat and hfsplus modules compiled for this to work of course. Check my Linux 1394 guide for getting the disk to work under Linux.