projects is meant to be a collection of few significant things. The main page for projects inlines "all" of them, but it has no way of knowing which parts of each project to inline, so it only inlines the front page of each.
bits is meant to be a collection of many insignificant things. Some of these entries are organized hierarchically into something approaching categories, or months and years. Intermediate entries (like "2007/") are structural in function and are not inlined -- only "leaf" entries are. Similarly, "support" files like illustrations are not inlined (anything which has "support" anywhere in any part of the filename doesn't get inlined).
I frequently think of things to add to entries after I write them, like to see what the entry looks like before publishing it, and so forth; on the other hand, I usually expect someone to only read the "finished" product. For this I have a ?scraps directory -- feel free to add it to your RSS reader, paw through it, and so forth, but don't expect that anything you see there is final. One day I'd like to have support for making RSS feeds out of commits to the wiki, but I expect that will be much less interesting than just seeing new finished products.
All files are in lowercase. I like to title pages with capitals, so all pages that aren't appropriately capitalized have [[meta title="blah"]] tags.