Um...what?
What is the flowchart for? As a substitute for GameFAQs? Or are you confused by the story and thus looking for a handy reference of key points? Although if the story was fairly linear that wouldn't be a very interesting flowchart.
I don't know what's happening here, so my list is
Castlevania: Portrait of Ruin
Tomba 2
Kirby's Dream Land
Seiken Densetsu 3
Bonus points if you can figure out why these need flowcharts