I use <projname>/src with subdirectories mirroring the modular structure of the system to build (roughly one subdir per namespace) and <projname>/doc for doxygen-generated sourcecode documentation. Makesystem is vanilla gnu autotools (autoconf, automake, libtool), but without recursive Makefiles, which are a Bad Thing^TM. Thus there are the usual README, configure.ac, Makefile.ac etc. in <projname>. Version control is by CVS, if needed.

.o-files, libs etc. just fall wherever the system drops them, which isn't a problem given that you can remove them anytime with make clean. On a particularly nasty machine where I have to try several compilers from time to time, I create build-subdirs like <projname>/sCC and do my ../configure && make there, so all binary stuff stays separated.

There is no additional manuals besides what doxygen dumps out, but if there where, I would stuff their sources under <projname>/doc/manual or similar.