Here is an archive of all the past top five lists I've done over the years.
For Marvel's two most popular characters, Spider-Man and Wolverine have had a surprisingly low amount of notable team-ups. Here are their top five (NOTE: I decided not to count the Ultimate versions of their characters).
Spider-Man Comic Strip
In 2009, there was an extended team-up between Wolverine and Spider-Man when the mutant decided to visit Manhattan...
Wolverine even tried to pick up Mary Jane...
Luckily, that actually helped protect Spider-Man's identity, because when MJ showed up at the end of the story arc, when Doctor Octopus had Spider-Man captured, Spidey was able to convince Wolverine that she was really there to see Wolverine!
Marvel Team-Up #117
In this story by J.M. DeMatteis, Herb Trimpe and Mike Esposito, Professor Power captures both Wolverine and Spider-Man and they have to fight their way out against some robots.
Bret Matthews and Vatche Mavlian put together a pretty basic Spider-Man and Wolverine team-up in Japan. Nothing much to talk about here, which was a shame, as Matthews has written some excellent Lone Ranger comics and some excellent TV shows in the Whedonverse.
Web of Spider-Man #29
Jim Owsley, Steve Geiger and Art Nichols did a story that was basically just a way to have Wolverine tell Spider-Man not to blame himself for what happened in Spider-Man vs. Wolverine. It did that well, but it's not much in the way of a team-up.
In this Todd McFarlane written and drawn arc, mostly referred to as "Perceptions," a Wendigo is on the loose, but Wolverine believes that this particular Wendigo is innocent of the killings it is being accused of. So Spider-Man agrees to team-up to help find some measure of justice...
5. Savage Wolverine #6-8
Zeb Wells and Joe Madureira deliver a fun storyline that does a good job playing with the contrasting nature of Spider-Man and Wolverine's personalities.
4. Marvel Comics Presents #48-50
Erik Larsen showed off his skills as a writer/artist with this arc (along with inker Joe Rubinstein), where the two heroes team-up and he gets in some interesting commentary about the very nature of superhero fights...