I checked with lintpkgsrc -S, and the following packages are not listed in
SUBDIR (in the category's Makefile) 

wm/fvwm-devel
pkgtools/libkver
pkgtools/libnbcompat
pkgtools/mtree
lang/php5
pkgtools/pkg_install
pkgtools/prereq-readme
devel/swig-build
x11/wxGTK24
pkgtools/xpkgwedge

This is the list for pkgsrc-2005Q2, although I don't know whether it's
worth a pullup: 

emulators/compat11
mail/cyrus
www/firefox-bin-realplayer
wm/fvwm-devel
pkgtools/libkver
pkgtools/libnbcompat
pkgtools/mtree
lang/php5
pkgtools/pkg_install
pkgtools/prereq-readme
devel/swig-build
pkgtools/xpkgwedge

GH