From my experience of playing D/P/Pt, I have accumulated some actions that cause the game to save a lot of data...
- defeating gym leaders/ advancing in the story
- catching Pokemons
- going to new routes / places
- having your game on for a long time
- filling a pokedex entry
Bulbapedia has some occasions on why it says 'saving a lot of data' instead of the usual 'saving'. Click here.
I will add more as I find them along the way.