Kirby,
I've tried all sorts of different organizational schemes - managed, referenced, folders, sub-folders...projects...
I feel pretty comfortable with the one I am using now. I have it set with top level folders that are pretty general - Holidays, Birthday, Outdoors, Travel, Special Occasions, etc... I have found it best to stick with one level of folders, which then contain their appropriate projects. Once something doesn't fit, I just create a new top level folder.
I can't recall why I moved to this, but I think it had something to do with the way projects were displayed in the Projects pane. It just simplifies things. I had tried using lots of sub-folders at one time and it just didn't work for me.
I typically name my folders as described above and then name the projects that are kept inside of them by date_name. So, mountain biking pics taken on June 9, 2011 would go into the folder, Outdoors, and be placed in a project named, 2011-06-09_Biking. This is just an example. I have found it easier to keep track of things when using this convention. I don't typically like to put the year first when naming by date, but it is the only way to keep things purely sequential. For example, 03-11-11 would come before 06-02-10 even though the latter is chronologically earlier.
I have also played around with the naming of my images a lot. I'm really just looking for the most efficient work-flow, but I also want something that is going to provide simplicity in the long run. I usually name my images with image date_custom name_Index. I had been renaming the masters in this fashion too, but have since questions whether I want to continue to do that. I do not like when I have multiple images with the same name - IMG_0024, for example. This happens quite a bit if you use Auto_Reset for the naming convention on your camera. I also felt that if I used continuous naming, that after 9999 on my camera, things would reset back to 0001. I'm torn as to how to continue, and while I know it really doesn't matter that much in terms of being able to know my images in Aperture, I'm kind of anal about this kind of stuff.
One issue I find with doing this is that it negates the "Do not import duplicates" function built in to the import function. This wouldn't matter if I always had a fresh card, but sometimes I don't delete my older images from my card before shooting again.
Any advice on file naming and work-flow would be appreciated. I'd like to hear what you have to say on the subject.