That's actually kind of tough. But here is what I would say.
5) Godzilla's Gigantic Leap and Body slam on Megaguiras: Some thought this was silly, and it was, but I liked it. It's the Godzilla vs. Megalon "Super Dropkick" of our day, and it will be remembered fondly years from now I think.
4) Final Wars' Final Battle: I remember the first time I saw the movie, I went nuts when Monster X turned into Kaizer Ghidorah. That think looked bad ass! The previous action between Godzilla, Monster X, Gigan, and Mothra was pretty fun to (but boy is Gigan stupid or what?)
3) Godzilla vs. Mechagodzilla and Mothra from Tokyo SOS: Visually, Tokyo SOS is the strongest Godzilla film in existence and the battle between the three kaiju superstars is a great showcase of special effects and action.
2) Godzilla appears to confront the UFO in Godzilla:2000: This might not seem like much to most fans, but G2K was the first Godzilla movie I ever saw in theatres, and when I saw Godzilla come out of the ocean with that oh so familiar Ifukube theme playing, I felt like I was five years old again. It was really special to me.
1) Climatic Battle from GMK: Godzilla takes on both King Ghidorah and Mothra with the military interfering throughout. This was an awesome scene for several reasons. Visually, its amazing. We also got great action out of too. Also, I loved seeing Godzilla just over power and destroy Mothra. In the previous encounters between the two monsters, Mothra almost always won, and even when Godzilla defeated Mothra in GvsM64, that was only because Mothra was dying to begin with. In this film, I finally got to see Godzilla squash the bug, and it made me happy. I also liked how Ghidorah became more and more powerful as the battle progressed. There is one shot during their fight where Ghidorah is in the air flying and glowing in a golden light, with Godzilla (back turned to the camera) with his spines glowing blue ready to fire. This shot is also at night, and it is really an awesome visual, if only for a few short seconds.