Dan Slott was nice enough to share with fans on Formspring his personal choices for his Top 10 greatest stories ever told. I asked Dan if I could share his list with you folks here, and he said, "Sure," so here ya go - Dan Slott's personal picks for the Greatest Dan Slott Stories Ever Told (with commentary on each of the stories by me)!
I'll include in brackets if the story ranked on the reader's choice for Slott's Greatest Stories Ever Told
HONORABLE MENTIONS: BIG MAX #1, SUPERMAN ADVENTURES #57, AMAZING SPIDER-MAN #600, SHE-HULK #2, JUSTICE LEAGUE ADVENTURES #11, MIDNIGHT SONS UNLIMITED #9, GLA: MISASSEMBLED, The GLX-MAS SPECIAL, REN & STIMPY #6, The POWDERED TOASTMAN SPECIAL, THING #4, LOONEY TUNES #75, LOONEY TUNES #93, AVENGERS: THE INITIATIVE #6, and the Blackjack stories from AMAZING FANTASY vol. 2 #15
10 BATMAN ADVENTURES #10-#13 back-ups: “Cats Game”, “Questions That Begin with a Queue”, “The Hidden Display”, and “Knight Light”. [Unranked, but his lead story in Batman Adventures #14 was #10]
These were a series of charming back-ups, including the final one, "Knight Light," about a kid who thinks he has a monster under his bed...and he might be right!!
9 THING #7: “Dis Man, Dis Monster, Disarmed” [Thing #1-8 was #8]
In this clever time travel storyline, the Thing tries to woo Alicia by taking her back in time to see the Venus di Milo. Hilarity, as you might imagine, ensues (especially when the Thing encounters Hercules in the past - a Hercules who has not yet met Ben Grimm). Kieron Dwyer did the art.
8 ARKHAM ASYLUM LIVING HELL mini 
In this gripping series, Slott and artist Ryan Sook (eventually aided by inkers Jim Royal and Wade von Grawbadger) gave us some fascinating insights into the minds of some of Batman’s deadliest rogues, as well as introducing us to some intriguing new ones, as well!
7 SHE-HULK Vol. 1 #4: “Web of Lies” 
In perhaps his first classic issue of She-Hulk, Slott has Jennifer Walters represent Spider-Man in a libel suit against J. Jonah Jameson. A hilarious issue with great art from Juan Bobillo and Marcelo Sosa.
In this epic storyline, how does Spider-Man deal with a situation where nearly all the citizens (not to mention the superheroes and supervillains) of Manhattan suddenly have the same Spider-Powers that he does? This was an ambitious and spread-out story that Slott managed to coordinate with other writers to form one of the most coherent major crossovers of all-time - while also still being a good story! I can imagine why he'd be so proud of it.
5 JUSTICE LEAGUE ADVENTURES #11: “The Moment”
This touching story sees the villain Chronos wreck havoc on time itself in an attempt to save his brother from a fire. The Flash and the Atom have to stop Chronos, but can they bring themselves to do the deed when the end result is that a good man WILL die? Min S. Ku and Dan Davis did the artwork.
4 MARVEL COMICS PRESENTS #116: Two-Gun Kid in “Just Deserts”
In this clever Two-Gun Kid story, Two-Gun Kid has to march a prisoner all across the desert...with a twist. Besides the stand-out twist (which I still remember today how much it made the story standout when reading it), it is Gil Kane art! Gil Kane, people!
3 SPIDER-MAN/HUMAN TORCH mini 
In this delightful series, Slott examines the relationship between Peter Parker and Johhny Storm throughout the years in an amusing character-driven look at the pair in various stages of Marvel history. Ty Templeton and Nelson do a great job on the artwork. When the Human Torch died, Slott did not have to look far to capture the emotional impact that it would have on Peter, as Slott had clearly established as much in this series.
2 REN & STIMPY Special #3: “Masters of Time & Space”
If you thought Spider-Island was an ambitious tale, then you will have to read Ren and Stimpy: Masters of Time and Space to believe it! The problem is, it is out of print and extremely difficult to find a copy. In any event, the story (with art by Mike Kazaleh) was a "Choose Your Own Adventure" tale (you know, if you want Ren and Stimpy to do X, go to page 5. If you want them to do Y, go to page 6, etc.). That is just the start of it, though, as the story is hilarious and also very, very very complicated (as time travel plays a major role in the story). I can't imagine how long it took him to plan out
1 AMAZING SPIDER-MAN #655-#656: “No One Dies” Parts 1 & 2.
In this poignant two-parter, first Peter Parker spends an issue confronting himself with all of the people he has known who have died over the years (after a brutally wordless funeral for a longtime supporting cast member). This leads to him deciding that, rather outlandishly, he won't let anyone die anymore under his watch! He makes this proclamation just as a new villain debuts who uses death AS his gimmick! So what can Spider-Man do when a bad guy's whole set-up is finding different ways to kill people? That is the challenge that Slott must find an answer to. The two issues are both drawn by Marcos Martin. Martin does a great job on the second part, but the first part (where Peter dreams about all those that he has lost over the years) is some of the best art you'll ever find in an issue of Amazing Spider-Man. Simply stunning stuff. This two-parter stands out in its mixture of heartfelt personal examination mixed with slam bang superhero action - really well done.
Thanks again to Dan for sharing his picks with us! Very cool of you.