Consider also safety. An internally-mounted drive is less likely to suffer spills, cord-snags, bumps, and other abuse.
Assuming your PCs PSU is of decent quality, the internal drive will likely be better protected from power anomalies as well.
Finally, an internally mounted drive requires no additional space.
In all sincerity, I use both on my rig. I have a 120GB SSD for my OS and applications, I have a 1.5TB HDD for my media/document storage and I have a 1 TB portable external drive to backup files and transfer them from my desktop to my laptop.
I also use hosted storage through Microsoft's skydrive for an additional layer of backup. I use this mostly for family photos and tax documents that I don't want to lose in the event of a disaster.
You may not need to do both, but at least for me I feel much safer about a hard drive failure not crippling my music collection or an additional deletion taking out a photo.