Well it's really a price and/or glossy screen issue.
The Mini is less powerful, like a laptop in a desktop case, hard drive is replaceable, it's for use with other monitors like anti-glare and existing hardware from a desktop PC.
Some use a KVM (keyboard, video, mouse) switch from both the Mini to their Windows 7 tower.
The iMac is a all in one device, if anything has a problem your taking the entire machine in for service. AppleCare is mandatory and living in close proximity to repair is likely essential. The cost of ownership of a iMac is quite high, once it goes down after your 3 years of AppeCare are over, your buying a new machine rather than paying to get it fixed in most cases.
If your considering the Mini, then your on a budget most likely and the better choice for long term value as you can easily replace the external parts like the monitor and hard drive. Which you can't do in the iMac.
As long as you have all those other Apple devices, why not get them both!!! Just kidding.
I was wondering the same myself. The specs aren'y hugely different between the two so I'll most likely opt for the all in one design. EXCEPT - the iMac is not really an all in one design anymore without the Super Drive.