Being somewhat off topic it's as good a place as any, another forum may have been Hardware & Devices
The main concerns for hard disk drives (HDD(s)) are having a magnet nearby, moisture, static/shocks and jarring vibrations as long as you can satisfy the absence of those conditions your HDD should be okay.
At the very least I would keep it in a resealable anti-static bag
that would help with the static and moisture. These are a little pricey, you might want to check with local computer shop to see if you can buy only one. An added help for moisture would be those silica desiccant bags
. You'd still have the vibrations and magnets to worry about, but they would have to be really strong magnets, ones that are used to close a clasp on a bag or pouch should pose no problem.
Normal vibrations while commuting should be okay. A jarring incident would be if your commute was involved in an accident or you dropped your bag more than the distance from your hand.
Knock on wood!
If your HDD is a "traditional" type with platters one problem may be going through any type of security check while commuting, the scanning devices used can emit very strong electromagnetic waves that may harm it.
If it is a solid state drive or the type that uses flash memory it should be unaffected by magnets like your iPod Touch but I'd still be concerned going though a security check.
According to the TSA here in the States the equipment they use does not pose a danger to electronics: "Checkpoint Friendly" Laptop Bags | Transportation Security Administration
There are HDD pouches you could look into that would cover most concerns they range from a 2.5" to the 5.2": External Hard Drive pouches - Newegg.com
I realize I have painted a worst case scenario, but if yours is a HDD that was built as an external you should be okay as they are designed with better features. Have you just started traveling with the HDD or have you been doing it for awhile?