If I am building a HTPC that I may upgrade to a gaming machine later and want a better gpu, should I completely stay away from Micro ATX? I just don't want to have any problems in the future with a part like a GPU simply not fitting in with all the other components. I know its not the same thing, but I had a Dell with BTX mobo once before and that was a pain in the butt to find replacement parts for, and I just don't want to go through that again.
I've been researching micro ATX gaming rigs and performance rigs for the past two days and I'm actually really impressed with what I'm seeing. Just search around for "micro ATX gaming" and other searches similar to that... for example thermaltake I believe makes a case called the lanbox.. such small cases were intended for portable gaming. So maybe you'll be able to find some answers within that research.
The past few hours... (and yes I know it's 5:30 AM..in NY at least..) I think I've come to settle with the Thermaltake A30 microatx case.
If you are talking motherboards, then the main difference is MicroATX boards usually have only one PCI-e X16 slot for a graphics card, whereas ATX can have as many as 4. If you are talking cases, then your concerns about fitment are justified. You have to be careful as some HTPC cases require a "low-Profile" graphics card, and a regular card will not fit.