Some here have already dwelved into this arena, some have looked, some have scoffed. But no one can deny there is a large allure for these small systems. Who can argue that small foot print cases like small footprint LCD monitors don't have good aspects? But it has a whole new set of rules.
I've gone from midtowers to SFF to midtowers and I am now again back to the SFF. You might think it disgraceful to limit you're overclocking, the amount of steel to be formed into a canvas being reduced by half or more may not sit well with you. But it suits me just fine. Don't think I'll be trading "up" again for a while. Sure she can't overclock well, my videocard isn't exactly top tier either. But she chugs along quietly, and cubic inch to cubic inch a helluva lot more fun. So lets look at what you can expect to gain (and lose) from a case diet.
Modding potential - it's all still there generally, but it takes a lot more deft skill to pull it off it seems, and requires more measuring and thought. When I fit 120mm side fans on my old Powmax mATX, I knew I could mount these suckers (or blowers) anywhere.
Power requirements - Many people seem to be able to install the most power hungry video cards on the market into their Shuttles with 250 watt PSUs, and still overclock their CPUs. But personally I like my 6600GT, I think it's a great small form factor videocard, it's short, it isn't anymore power hungry than my 9600XT was - but twice the performance for 220 bucks. Look into things like this when building a SFF.
Airflow - normally horrid, but that's why we've got modding skills. With mesh and 120mm fans, we can make anything cool well. Remember, with their smaller cubic area, you can "purge" the heated air out faster with less cfm. CFM to CFM in a theoretical world, a SFF case would actually cool better than a fullsized. But the key there is theoretical.
In the end though - you either love them or hate them, but if you're sitting on the fence give it a try. Small Form Factor for me is turning into a worse addition for me than free internet p0rn.
Iateronmly