I looks like I'm going to need to change my computer case. How hard is it to swap a motherboard (I know I can deal with the rest) between a flat case and tower style case?
As has been mentioned, making sure you have the same form factor is the biggest concern. However, you also need to consider any special design modifications that may have been made to accomodate the flat case that may not transfer over to a tower case.
For instance, the company I work for does extensive work with industrial panel PCs. These are ruggedized PCs built with a small, flat form factor and an integrated touch screen. Because of their specialized applications, they have a custom-designed motherboard which actually rests in the middle of the casing, with connections on both sides. If I may demonstrate with an ASCII portrait (you'll have to use your imagination):
**************************
Touch Screen LCD
**************************
Cabling to connect LCD and screen-mounted peripheral ports (USB etc.)
---||---------||-------------||-----
Motherboard
-------||-----------||------------||
Hard Drive, CD-ROM drive
_____________________|Power Supply|
OK, so I'm not Da Vinci. Still, the basic point is that, given the special form factor, these PCs have connectors on both sides of the motherboard, which would require special accomodation if I made an attempt to transfer it to a more standard case. It could still be done, but would require some physical modifications to the case itself, and probably be more effort than the whole thing is worth.
This is only one example of a possible complication; different manufacturers do different things, and sometimes you can end up with a tremendous headache. Assuming, however, that there is nothing particularly special about the original case or motherboard, transferring it should be fairly quick and painless, as long as you're handy with a screwdriver and can read the fine print on your connectors.