I have seen that USM #13 tends to do well on Spidey-centric lists and among USM fans (I think it probably was the best issue of the main series myself). Interesting to see that it did well on a comics in general list (wish that Pizza Dog issue from the Hawkeye series had been higher; that run was something special).
Outside of that number 13, my favorite single issue story I've read in the franchise was probably that first Spider Slayer back in Lee/Ditko classic ASM era; really fun premise down to the sheer lunacy of Spidey being chased by a robot with Jameson's face and the way Peter brings it all on himself with an ill-timed prank. They also revisited it for that great Spider-Girl story where Mayday travels back in time and meets her dad when he was her age.
Doctor Strange: "You are the right person to replace Logan."
X-23: "I know there are people who disapprove... Guys on the Internet mainly."
(All-New Wolverine #4)
Fred Hembeck had a great review of that one.
http://www.hembeck.com/Covers/Spiderman25.htm
Sincerely,
Thomas Mets