I just do it becasue it makes it easy to get to the one I am after when I do add reference :)  Plus I sometimes have the source + tooling there too (so for example the whole NUnit GUI and Console runner ... ) and there are hundreds of files

I just have to ask, why are u rebuilding your libraries?  

Are you making changes to Rhino/Windsor, etc.  If you are NOT then rebuilding them just seems like a waste of cycles.

I usually do have some features I am working on inside one of the sources, yes. Until recently there were some pretty invasive features I had in my local copy that wasn't patched in.

Plus, features I find interesting are frequently being added to one of the projects so I like to keep up with it. I have found it simpler to keep up with the changes rather than try to figure out all that has happened later on and really with all the work Ayende and company have put into the build process has made it so simple there isn't a reason not to.

if lib/ is your assembly location that projects reference, then I don' t see any problem doing this. i typically put all of my pre-compiled assemblies in a single folder like this, as well.

if you're talking about the source of these tools, then i think there's obvious reasons you want them each in their own sub-folder... it's easier to see what's what and not get confused with a bunch of different solutions in one folder.