I generally have enjoyed most of the missions throughout the trilogy, and absolutely love the missions that feature a really impressive setting with beautiful art and design having gone into that level. Arguably all of them do, but ones that immediately spring to my mind that stood out for me are Eden Prime (ME1), Virmire, Ilos, Dossier: The Professor, Kasumi: Stolen Memory, Dossier: The Warlord, Horizon, pretty much all major missions on Illium (including LotSB, I love Illium and Nos Astra as a setting!), Collector Ship, A House Divided, the Suicide Mission, and pretty much every Priority mission in ME3 as well as all the major side missions (not N7 ones, like Attican Traverse: The Rachni and the Ardat-Yakshi monastery).
These missions stand out for me for other reasons as well, story, combat etc. but its just how each have such iconic and beautiful locations and settings that just really stick with you.
Judging from the trailer for ME:A, there are already a host of interesting and impressive new locations that intrigue me, especially the one with the flying creature in the distance and the one with fiery tornadoes!