I recently purchased an external hard drive for my Wii U. I don't have much space to work with, and I currently have it setting on top of the wii (both of them are flat). I can't think of any reason why it would be harmful for either of them, but I thought I would check with other folks to make sure. I appreciate any feed back.

Thanks!

Normally I wouldn't recommend stacking any consumer electronics unless designed to operate that way.
Two things come to mind: heat, and electro-magnetic interference.
Good RFI shielding (FCC compliance) covers the latter, leaving only heat.
The Wii U runs incredibly cool so my only concern would be that there's no heat transfer from the HDD case to the Wii U and obviously that no vents are blocked.

My suggestion would be to ensure that there's some sort of air-gap between the two by fitting some stick-on rubber feet to the HDD case if you found that the HDD case gets warmer than the Wii U's.

Should be OK just don't come here making a 'My HDD and WiiU just exploded what should I do' thread

Me personally I would not stack anything on top of the Wii U. For one thing there are vents on top that can become blocked and could cause your Wii U to overheat. If you have limited space have you tried standing the Wii U on its side and maybe putting the harddrive next to it?