I fully support the notion that every module has its own directory.
* By putting modules into their own directory, we're making it easier for some of those comments.help related ideas to kick in - to stick the help text in an external file and call it only when needed. I also think that chx's splitmode is a lot nicer if we could constrain the split functions to their source directory instead of having a primary directory full of 1000+ mini-files.
I have the following on my list when HEAD is open for features again. We discussed it on the mailing list before, and an .ini file will have the module name and description. This avoids the need to load all module when the admin goes to admin/modules, and overcomes the memory issue associated with that. It also opens the door to putting in things like version number (not file version, but release version, date of change, and many other meta data, and nifty things). Split mode is nice performance wise, but would it be overkill in most cases?