The Punisher has had run-ins with Superman's partner Batman a couple of times. The Punisher's severe methods of crime fighting are even disagreeable with that of the Dark Knight.

DC/Marvel Crossover Classics, Vol. 2

Batman
Blade
Captain America 
Catwoman
Daredevil
Elektra
Fantastic Four
Green Hornet
Green Lantern
Incredible Hulk
Incredibles
Punisher
Robocop
Shazam 
Spiderman
Steel
Supergirl
Swamp Thing
Teen Titans
Teenage Mutant Ninja Turtles
Wolverine
Wonder Woman 
X-men