We keep data separate, organized at the top level or two by SDSFIE topics or in a few cases by owner. Layer files are kept with data.
Map projects and exported maps are also separate from one another. We can move map projects and output files easily, but moving data is always harder because of links.
Map projects and output are also organized by SDSFIE topic and owner, although those that are not meant to be permanent are usually stored in a "temporary" folder. I don't think there is any way to avoid some miscellaneous folders for maps or strange bits of data, especially with 3+ people creating them. I just periodically try to find better locations for them or to toss them.
Map projects that are more permanent (reusable) or that are good templates are stored higher up in the map project file folders. We often have an "older" and "one-off" and "testing" subfolders. We try to avoid updating these subfolder maps with new links or when software changes.
I also like keeping editing maps and some analysis maps separate from cartographic maps, not inside topic folders. They are too different and a little risky for anyone other than their creators or experienced analysts to use. They can be great documentation, though, because they can tell a story of how the data came to be, which is incredibly useful when cleaning up after a complex edit or analysis process. I start some of my editing maps over from scratch after major software or data changes (so they run better).
