The advantage of an external is that is portable, potentially storable off site, and can be used on various machines. Several makers have those enclosures and they are relatively cheap ($20-30) You can put any maker's compatible hard drive in there and get the same thing. It runs off USB 2 or Firewire usually.
I prefer internal because there is one less thing to fall off my desk, but that's my personal issue. Also why I don't use external CDRW, and external modems (when I used a modem).
I use my internal secondary drive to:
1) hold the image of my pristine system load AFTER all updates, service packs, etc and main programs that I will always use. Other programs can be installed again later.
2) Data
This is on my (uggh!) Windows system. On Linux I just backup my data to a CDRW, because I can install the whole operating system from scratch, if needed, in under 10 minutes!!!!!!!
2) Data