The GUI is no longer being built because the program "moc" can't be found. 
This is easy to fix by correcting the QTDIR variables in debian/rules

I attached a patch that fixes the version from sid (1.6.1-1). I enabled the 
doxygen-gui binary package in the rules and in the control file.

Cheers,
Philipp
diff -u doxygen-1.6.1/debian/changelog doxygen-1.6.1/debian/changelog
--- doxygen-1.6.1/debian/changelog
+++ doxygen-1.6.1/debian/changelog
@@ -1,3 +1,10 @@
+doxygen (1.6.1-1.1) unstable; urgency=low
+
+  * Non-maintainer upload.
+  * make doxigen-gui build again. Closes: #556263. 
+
+ -- Philipp Edelmann <edelm...@fs.tum.de>  Thu, 03 Dec 2009 13:59:26 +0100
+
 doxygen (1.6.1-1) unstable; urgency=low
 
   * New upstream version.
reverted:
--- doxygen-1.6.1/debian/control.doxywizard
+++ doxygen-1.6.1.orig/debian/control.doxywizard
@@ -1,15 +0,0 @@
-
-Package: doxygen-gui
-Architecture: any
-Depends: doxygen, ${shlibs:Depends}
-Suggests: doxygen-doc
-Replaces: doxygen (<< 1.2.14)
-Description: GUI configuration tool for doxygen
- Doxygen is a documentation system for C, C++, Java, Objective-C, Python, IDL
- and to some extent PHP, C#, and D.  It can generate an on-line class browser
- (in HTML) and/or an off-line reference manual (in LaTeX) from a set of
- documented source files. There is also support for generating man pages
- and for converting the generated output into Postscript, hyperlinked PDF
- or compressed HTML.  The documentation is extracted directly from the sources. 
- .
- This package contains doxywizard, a GUI configuration tool for doxygen.
diff -u doxygen-1.6.1/debian/rules doxygen-1.6.1/debian/rules
--- doxygen-1.6.1/debian/rules
+++ doxygen-1.6.1/debian/rules
@@ -2,14 +2,13 @@
 
 #export DH_VERBOSE=1
 export DH_OPTIONS=
-export QTDIR=/usr/share/qt4/QtGui
+export QTDIR=/usr/share/qt4
 
 DEB_BUILD_ARCH ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH)
 with_doxywizard := yes
 ifeq ($(DEB_BUILD_ARCH),hurd-i386)
   with_doxywizard := no
 endif
-with_doxywizard := no
 
 CFLAGS+=$(if $(findstring debug,$(DEB_BUILD_OPTIONS)),-g)
 CFLAGS+=$(if $(findstring noopt,$(DEB_BUILD_OPTIONS)),-O0,-O2)
diff -u doxygen-1.6.1/debian/control doxygen-1.6.1/debian/control
--- doxygen-1.6.1/debian/control
+++ doxygen-1.6.1/debian/control
@@ -38,0 +39,15 @@
+
+Package: doxygen-gui
+Architecture: any
+Depends: doxygen, ${shlibs:Depends}
+Suggests: doxygen-doc
+Replaces: doxygen (<< 1.2.14)
+Description: GUI configuration tool for doxygen
+ Doxygen is a documentation system for C, C++, Java, Objective-C, Python, IDL
+ and to some extent PHP, C#, and D.  It can generate an on-line class browser
+ (in HTML) and/or an off-line reference manual (in LaTeX) from a set of
+ documented source files. There is also support for generating man pages
+ and for converting the generated output into Postscript, hyperlinked PDF
+ or compressed HTML.  The documentation is extracted directly from the sources. 
+ .
+ This package contains doxywizard, a GUI configuration tool for doxygen.

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