I rarely work at colaboratable projects that have many changes at codes (more than wikis), but when I do, I suggest using GitHub For Windows+Git+GitHub for open source projects, or TortoiseHg+Hg+BitBucket for non-opensource projects. I have tools that export the RPG Maker XP project into Yaml files (for maps, events, tilesets data) and rb files (for script editor source) for better viewing the code using these tools, although only the last one is really useful, plus the PBS. Anyway, I never use these export tools on a real project.
Initially, I made my code only to myself, so I used too many acronyms and other bad practices like too many code duplicity. Now, I put several comments, auto-explanatory variable names, including Design Patterns names (like Builder/Helper/Factory) and so on. I too, group trainer parties by location in game. Sometimes I try to document certain things that aren't easy for checking like the items at each area or the party that I used to beat certain boss (for balance purpose).
I prefer to use big tilesets with the buildings and others objects setted, and, when I add new tiles, I sometimes try to fill spaces that are left, especially when I have one/two tile objects.
When I first made the Pokémon Shop at my game, this system consisted of several copy+paste code/commands, so changing a pokémon requires too many duplicity to be rewritten. A year ago I rewrote this part, now all that I need to do is to change an symbol array, that also can be accessed by other methods and checkings if I wish.
