Rob,
My apps (along with all other non-OS related files) are on a seperate partition for 2 reasons:
1. The partition is FAT32 (so that I can see the files on my Win98 machines at work and at home)
2. Preventing data fragmentation- since I wont be doing much (if any) moving, copying, etc... of...
Rob makes a good point about having the swapfile on a seperate drive as opposed to having it reside on the same drive. This is actually a better setup than having it on the same drive.
The most important thing overall is to have a seperate partition for your OS, and a seperate partition for...
The smart way to set up a system is to have 1 partition for your Operating System and then another partition (or multiple partitions) for your applications. I set up all of my systems like this: for example, my Laptop setup:
Partition 1 (boot): LILO
Partition 2 (primary): Linux
Partition 3...