These may change, but as of right now they are:
1) King Kong vs. Godzilla (1962). The reason for this is because it basically put Godzilla on the map; plus, it has arguably the best monster fight in Godzilla history, which is another large and important part of Godzilla.
2) Mothra vs. Godzilla (1964). This film has another great monster battle, but it also has a very enjoyable story. The reason for stating that is to show that even a monster movie can have a good story behind it; in other words, it stamps out the stereotype that all giant monster flicks are nothing more than guys in rubber suits.
3) The Mysterians (1957). I chose this film because it is important in that it helped set the blueprint for what is one of the most popular themes in monster movies: alien invasion. While not being the best alien invasion movie, it is very important in establishing the concept for some great Toho monster flicks to come.
Each of these movies I chose because, to me, they were very important in molding Japanese monster movies into what they have become today. Gojira is an important film in Toho's history, but in my opinion, that particular film is more of a message to me. That is important, but not what made the series popular, in my opinion.
*Side note* I was going to put Godzilla vs. Megalon on this list for the camp factor, but decided against it because that isn't really an important aspect of these movies. That's not to say they aren't fun as can be though.