I consider trilogys that are one long story to be one film, like star wars. While trilogys like Indy are 3 separate films. So....
1. Back to the future trilogy
2. Star Wars saga
3. Indy and the last Crusade
4. Godfather trilogy
5. Raiders of the Lost Ark
6. Stand By Me
7. Forrest Gump
8. T2
9. Lord of the Rings
10. Braveheart (If it was historically correct it would be much higher)