Eyefinity certainly still has its own issues that need to be worked out.
But as others have said, WSGF is the best place for information at the moment to get everything working.
The active adaptors are still too expensive, they cost $150 in Canada.
Bezels and viewing angles. Viewing angles are more of a problem when all monitors are in portrait mode.
Multi monitor stands cost more than the monitors typically.
Bezels certainly could be smaller. Though not actually as big a problem as most people would think.
Stretching when using high aspect ratios (3x1 landscape), in some games it's unbearable.
I currently run three Samsung 2343 2048x1152 monitors all in portrait mode on a single 5770. It's quite impressive, but after a $1000 investment ($200 per monitor, $150 for the adaptor, and whatever I paid for a 4870 then paid some more to traid it for some guys 5770), I think I may have been better off going for a 30" 2560x1600 or a 50" 1920x1080 plasma.
I just haven't found multimonitor a viable option in gaming, but I do enjoy it for desktop usage. (Email and IM on one monitor, browser on the other, xbox hooked up the the third for some FF XIII lovin').
I am a multimonitor believer, and I think by the 6xxx series cards most of the issues will be fixed, and it should be perfected by the time the 7xxx cards release.