I'm breaking this into two parts, as both come to mind when I see this phrase.
Best ones that shows what a Graphic Novel can do:
American-Born Chinese: This simply could not have been told in such a comprehensive way nor in such a touching way by any other means. The fact that the bright colors and comic aspect will draw readers in who would never read this type of book otherwise is a huge bonus.
The Sandman: The Dream Hunters: If you like Neil Gaiman and even if you've yet to read The Sandman series (which if you like Gaiman and haven't, you should at least once), you HAVE to check out this Graphic Novel! I can't express how gorgeous the pictures are in this. I read this and immediately bought the hardcover version of it even though I don't own any other Sandman books mostly because of the artwork.
Favorite Graphic Novels:
Avatar The Last Airbender - The Promise: This is the hardcover collection of three or four smaller versions that together make up one story. The hardcover also has annotations from both the author and illustrators. I loved it and can't wait to get the next one.
Star Trek IDW Vol 7 - The Khitomer Conflict: I like this whole series but this one in particular just blew me away. Taking place soon after the events of Star Trek Into Darkness, it was exciting and opened up all kinds of interesting ways for the crew to go. I'm looking forward to seeing what comes next.
One Piece: I love this whole series; it's easily my current favorite manga.