I personally really liked how both FMA and Eureka Seven turned out visually. Their animation and art (especially in E7's case) was always very clean, colorful, and fluidly animated, and they never skimped out anywhere - it was consistent between the slow, quiet scenes and action scenes. They were decent about details, too - obviously nothing close to Ghibli in that aspect, but good nonetheless. But then again, I like BONES.
Full Metal Panic was pretty good for the first two seasons, I'd say a bit above average, but in FMP: The Second Raid, it was quite obvious that they had a significantly larger budget to work with. The quality was very good in that series, at least in my opinion.
Serei no Moribito is a visual masterpiece despite slight overusage of CGI.
I'm currently watching Clannad in HD and honestly I'm stunned by it. Every scene is very beautiful, flawless, and fluid. The sequences featuring the girl and the little robot thing are a treat too thanks to the hypersmooth animation caused by the boosted framerate during those periods. Are the rest of the Key-based animes like this as well? If so, I need to get busy tracking down those torrents...