Here is my own personal Top 10 list of my favorite Japanese kaiju made in 1999 when I was 16!

#1 Godzilla
The King of the Monsters is obviously my choice for #1. The star of 28 films, protector of Earth, destroyer of cities, the most powerful being on the planet, the list goes on and on. He is the result of man's destructive power a.k.a. the Hydrogen bomb. Once Godzilla starts a fight, he will not stop until he either wins, or is temporarily defeated. Thanks to his super regenerative powers, heat ray, strength, and attitude, Godzilla has defeated pretty much every kaiju the he's gone up against at one time or another. Godzilla has appealed to every generation in one way or another, whether it was his destructive/revenge attitude of 50's, early 60's, the Heisei series, the new millennium films, and Kaneko's film, or if it was his protector or Earth/hero attitude of the 60's and 70's, Godzilla has appealed to everyone, young and old.
#2 Anguirus
Anguirus and his never-say-die attitude make him my #2 choice. Anguirus is one of the most impressive kaiju I have ever seen. He will challenge kaiju twice the size or strength of him, he gets knocks down, but gets right back up and attacks again more vicious than ever! To a lot of fans, Anguirus is a lesser kaiju since he has no energy beams or projectile weapons, but to me, he is a nearly invincible force of viciousness and fury. Anguirus has complete and total loyalty to Godzilla as was proven in Godzilla vs. Gigan and he could possibly be returning soon to the Godzilla series.
#3 Rodan
Rodan used to be my #2 favorite of all kaiju before I really paid attention to Anguirus, but he is my #3 favorite kaiju non-the-less. Rodan, another symbol of nature striking back at mankind, is a very impressive kaiju to me. I liked him best in the original Rodan, where he also looked the best. Over the years, Rodan has fought both alongside and against Godzilla, and proved to be a very formitable opponent for the King of the Monsters back in 1964 before they teamed up to take on King Ghidorah. Rodan never received much credit in kaiiju films other than his first film in 1956. He basically played second banana to Godzilla in the films he starred in after the original movie, but he is a very impressive kaiju with a dare devil type attitude, as represented in Ghidorah: The Three-Headed Monster when he rammed head first into King Ghidorah at Mach speed.
#4 Gorosaurus
OK, now #4, Gorosaurus. I can't really explain it, but this kaiju just clicks with me, maybe for the same reason Titanosaurus clicks with some people. He is like most dinosaurs, except bigger and a lot meaner. He has Anguirus's never-say-die attitude which he used when he and the other kaiju battled King Ghidorah on Mount Fuji in 1968 (or 1999, whichever you prefer). Another thing that really impresses me about this kaiju is that he has an incredible move, his kangaroo kick. He has even knocked over King Ghidorah with that devistating kick!
#5 Gamera
The Guardian of the Universe is #5 on my list. Mainly because he, like wine, improved with age. His later films (Gamera: Guardian of the Universe, Gamera 2: Advent of Legion, and Gamera 3: Revenge of Irys) really impressed me as did the giant turtle himself. He is deprived of super-fast regenerative powers (his are rather slow), and yet still sacrifices his body to save the planet. The best example I can think of was in Gamera 3 when he severed his own hand to stop Irys from sucking his life-force and finally finished off the tentacled kaiju. If he hadn't improved from his older movies, he more than likely wouldn't be my #5 favorite.
#6 King Ghidorah
Of course, #6 is King Ghidorah, the most beaten and reused kaiju (next to Mothra) in the entire world of Japanese giant monster films. He is the most reacurring bad guy in the whole Godzilla series. Impressive in both size, strength, and looks, King Ghidorah will take punishment and come back for more. He sometimes will win a battle, but eventually loses in the end.
#7 MechaGodzilla
Godzilla's robotic counterpart is #7 on my list. My favorite is the 1993, G-Force version of MechaGodzilla, a very powerful robot that actually managed to kill Godzilla, but lost in the end thanks to an assist from Fire Rodan. MechaGodzilla has a huge arsenal of weapons, which makes him one of the most powerful kaiju Godzilla has ever faced. Not many kaiju have faced MechaGodzilla, but he could probably take many of them on with success.
#8 Titanosaurus
I used to not like Titanosaurus very much, but thanks to Andrew Shields, I've come to like the aquatic dinosaur more and more over the past few years and he has worked his way up to #8 on my list. He is deprived of energy beams, but can create hurricane force winds with his webbed tail. He is one of the more interesting kaiju with his bobbing head, strange roar, and the fins lining his back. Titanosaurus has appeared in only one film, but has still gained a lot of fame.
#9 Megaguirus
My #9 is Godzilla's fastest and most agile foe, Megaguirus. This kaiju was a great addition to the Godzilla series. Megaguirus is so fast that it even took Godzilla a while to catch up to him and take him out once and for all. I particularly like his evil and cunning attitude as seen when he was flying around Godzilla and when he was about to drop that big piece of building on his head. I hope one day Megaguirus returns to battle Godzilla once again. I'd also like to see Megaguirus go 1-on-1 with Rodan.
#10 Destroyah
My #10 is the side effect of the oxygen destroyer used on Godzilla back in 1954. I particularly like him because he transforms from one form to another. Be it his crab form, flying form, or final form, he is a very strong kaiju. Even though his final form is rather bulky, he could still dish out a ton of punishment to Godzilla and Godzilla Junior when they fought in 1995. Destroyah has his weak points though, especially in his final form (spurting blood whenever Godzilla hit him). Even though Destroyah was killed by Godzilla, he still may return someday to try and get revenge on the King of the Monsters.