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BN's right - pencil and paper are the best way to go. Don't be afraid to get messy. I would personally start by drawing the GUI, then pull out every single element (both tangible, such as the player, enemies, and inventory, and non-tangible, such as movement, combat etc.) and detail exactly how they work. If you'll be using a database, draw an Entity-Relationship diagram. Draw pictures, write pseudocode, and do anything else you think might help before you even touch the compiler.
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