Yes, i saw at least two or three P99s in Xmen two. Styker's right hand man, played by Peter Wingfield (Methos from Highlander TV series BTW) had a P99 i beleive as well as a few others.
The white house guys at the begining of the movie all had sigs, it looked like , and the cops and Glocks...
Back to Matrix Reloaded: that was one well armed movie!! Morpheus' Glock 18 and Walther P99, Trinity with her usual Berretta 92. The agents with the desert eagles......and that Twin thing had a HK UMP machine gun.......nice......
I think that just about covers all the firearms.........then we have to talk about that Paul Chen Musashi katana that Morpheus used......those Sais Neo used...........How about that Ducati bike Trinity used? she sorta used it as a weapon..........hehehehe