Its mostly a personal preference as to how many partitions you want. People use partitions for various reasons. I also have a 40GB PATA and an external 200GB HDD. Here's how I went about storage
Partitions on the 40GB HDD
1. 13GB Primary Partition - WindowsXP, Progam Installations
2. 10GB Partition - Programming Data
3. 15GB Partition - Music
Partitions on the 200GB HDD
1. 73GB Primary Partiton - Movies
2. 73GB Partition - Music
3. 40GB Partition - Games / Files etc
As you can see, its just how you want to organize your data. Its not recommended to keep too many partitions, and also having no partitions could cause file fragmentations to be spread across the entire disk.
Cheers
Aditya