Jimmy "The Tulip" Tudesky (Bruce Willis) uses a Ruger P89 as his weapon of choice in the film.
Walther PPK
Jill St. Claire (Amanda Peet) chooses a Walther PPK from Jimmy's collection as her weapon of choice in the film. Do to her lack of clothing during the scene she is seen mainly using it, the shots had to be censored to follow the rule and regualtions of the site. Quoted from the film as Jimmy and her discuss the gun:
Jill: You don't like the Walther?
Jimmy: I think you should go with what you're comfortable with.
Jill: It's what James Bond uses.
Jimmy: Really?
Jill: Yeah.
Desert Eagle
Franklin "Frankie Figgs" Figueroa (Michael Clark Duncan) uses a nickel plated Desert Eagle (which looks like a flashpaper prop) as his weapon of choice in the film, although he never fires it.
Smith & Wesson 5904
Two Smith & Wesson 5904 pistols are seen on Jimmy's table when he has all his weapons sprawled out and Special Agent Steve Hanson (Harland Williams) keeps one as his issued sidearm.
SIG-Sauer P228
Janni Gogolak (Kevin Pollak) uses a SIG-Sauer P228 fitted with a sound suppressor when he goes to kill Jimmy in his house. Later, Sergeant Buchanan (Sean Devine) is see drawing his P228 when he enters Jimmy's house after the shootout.
Glock 17 Pro
One of Janni's thugs is armed with a Glock 17 fitted with an extended barrel to thread a suppressor, implying it is a Glock 17 Pro.
It's not a Glock 17 Pro. It's just a regular Glock 17 with a threaded barrel. That variant is only available in Finland, and it's based on the Gen 3 Glock (the one in the movie is Gen 2). I don't think the G17 Pro had even been introduced at the time the movie was made.
Makarov PM
One of Janni's thugs is armed with a Makarov PM fitted with a sound suppressor.
Questionable Luggage
Janni transports several guns hidden under his luggage to Montreal when he leaves Chicago in search of Jimmy. While airport security would likely have found this amount of weaponry hidden, movie logical contradicts this.