I see this time and time again. A member gets it in his head that he's going to make a game, then just like that the ideas are gone, the game is never made... why? you may ask... PLANNING.
I'm going to take you through my planning process and maybe, just maybe it will help someone, somewhere.
First and foremost I make a Design Document. In the design document I describe in frustrating detail every minutia of what I'd like in the game. Items, Weapons, Enemies, Cheats, ad infinitum, ad nauseam.
I then collect as much information as I can from various sources, be it Zelda Fan Sites to Player's Guides.
I currently own 4 players guides for Ocarina of Time and use them on a daily basis. I also use an emulator and map out levels on graph paper (10 : 1 inch).
Before even writing one line of code, I will plan out exactly what something will look like in Photoshop, MS-Paint or whatever graphics program I'm using at the time, this way I can get coordinates and simply write them in my Design Journal (VERY IMPORTANT).
I do not use constants in the game (except for colors and environmental variables) so that if something needs to be changed by say one or two pixels I can simply change it and reload on-the-fly.
I would suggest sticking with a naming schema as well and a well thought out Folder style.
When programming, I will ALWAYS comment my code... even if I'm the only one who's going to use it... this is just good practice.
This way I can come back to my code and know where I left off, etc.
Yes, GameMaker DOES have to parse through spaces and comments, so what I do is in my RELEASE versions I will remove any extraneous blank-space and comments by creating a copy of the current .gm6 file.
Here's a good practice too... make sure you have a folder with Backups, dated. This way you can go back to a version if you should "mess" something up.
PAY ATTENTION TO DETAILS: I can't stress this enough. Remember, these are Zelda Fans, they will catch the smallest problem and blow it up to gargantuan proportions
I'll think of more later.