well let's see

nge smurfed up my brain when i first watched it
code geass too smurfed up my brain and my heart
and lagann made me appreciate the fine art of GAR

so yeah, those 3 especially, left an impression much more intense than any other anime i've watched (and i've watched lots of sht)

special mention for Monster, which too messed up with my brain, but dammit if it isn't the most flawless-structured story i've ever watched