I love Game Maker Studio. It's definitely got all the power I need. However, I'm still very new to it (day 2) and am easily lost when looking for things I need and as a result it's hard to stay on track.
So I started using FreeMind to solidify and organize my program's structure and plan things out into a hierarchical diagram of states that I can refer to later when I'm bumbling around the interface and code reference manuals.
I use "!" symbols to indicate events. Down arrows are button press events, up arrows are release events, rocket ships are gotos, "?" are conditional statements with true-false actions indicated by checkmarks. Timelines are indicated with hourglasses.











