I've done a little investigation and it seems that:
/usr/include/ is commonly used in RPM-based distros (Fedore, SuSE, Mandriva)
/usr/include/tcl8.4 is used in DEB-based ones (Debian, .Ubuntu)
Furthermore, it turned out that we had a bug in configure.ac that prevented correct inclusion of tcl.h
It is now fixed in SVN.