SUP,
ive been running SFF for a while now and swear by em. yes. fitting a nice card is a big problem.
there are 3 things to consider really
Heat... is this going to put too much heat inside such a small case
Size... WILL IT FIT!
Power... Will your powersupply have nuff juice
as for heat... a higher performance card will cause more. you need to get that heat out of the case fast! adding more cooling by a blowhole or fan will help. it also depends on the grills you have on the side. Shuttle uses 2 types of cases here, one ith just a few rows of driled holes and one with big wire meshes. the messhed ones are better and you can buy em if you want to upgrade to it
now for size. 2 slot solutions are out. with the design of the cards and the shuttle, you can only fit the cards that only take up 1 expansion port so for some high end cards, you're S.O.L. and another thing is how much space will be between the case and the GPU cooler. some brands come with bigger coolers that are thicker. it may press up against the side of the case and choke it for air
power supply, gotta remmber shuttles only have a 240w power supply. now this is adequate for most uses, a high end card has big power draws. you might find that it will work, but other things might not!
I put a Geforce 6600gt in my previous shuttle and it worked ok. heat wasnt overly a problem, BUT room was cause the cooler pressed against the case, I had to drill out the side to allow it to breat cleanly. and as for power, i had a 220w version of a shuttle, and it was enough to power my card, but i lost the ability to burn DVD's. the draw was so much that there wasnt enough juice to burn them. could still read them and burn CD's, just not the extra juice needed for DVD's
hope this helps.