Please, please update the version number in source/include/version.h to include the versioning of your package. This makes it easier to distinguish standard samba builds from custom-build samba builds (distributions often patch packages). For example, a good version would be:

Version 2.999+3.0.alpha21-5 for Debian

Samba now has support for building parts of samba as plugins. This makes it possible to, for example, put ldap or mysql support in a separate package, thus making it possible to have a normal samba package not depending on ldap or mysql. To build as much parts of samba as a plugin, run:

./configure --with-shared-modules=rpc,vfs,auth,pdb,charset