I can't limit it to just five...so I'll do an old-fashioned Top Ten list:
10. State of the Art 2063 - Lots of good slice-of-life type things, and really helps make the world feel more real.
9. Shadowtech - The interactions between The Smiling Bandit and both Wolfman and KAM were brilliant.
8. Tir Tairngire - Lots and lots of fun stuff...but I'm a sucker for the IE stuff too, as well as Laughing Man

7. Year of the Comet - The story about the Shedim was AMAZING as was the development of Ghostwalker's takeover of Denver
6. Dragons of the Sixth World - Oh boy, where to start...lots of plotlines advanced, concluded, and started in this book. IMO it was the last of the Old School style books (Shadows of Europe felt a bit flat to me compared)
5. Aztlan - Three levels of awesome in this one. First is just the book itself, then the "additional commentators"...then just that tiny bit at the end which was the first hint we got of the otaku.
4. Threats - No other book has advanced so many metaplot story threads in so few pages. Brilliant work.
3. Portfolio of a Dragon - The will itself would've been enough to put this book in the top ten list, but the stories that followed...wow...
2. Renraku Archology Shutdown - The story of the little kid at the start is creepy as hell, and the development of the entire Deus situation was handled brilliantly. If I'm not mistaken, this was the first of the "entire metaplot story in one book" sourcebooks rather than previous plots which were developed over several books, a move which I feel damaged further books. Better from a game book standpoint (everything you need to run a plot in one single book purchase), but far worse for the storytelling as there's no more anticipation and speculation.
1. Universal Brotherhood - Wow...just wow...I can't put into words...this is just brilliant storytelling. I'm talking about UB itself, not the Missing Blood adventure. It has almost no game rules in it, no Shadowtalk, and the only familiar faces that show up became familiar later on (like Hatchetman). But oh my god...just brilliance wrapped up in awesome with an nice topping of epicness.