oops, I forgot to post the logs:

yakk@gir /gnome-source/GNOME2/gstreamer $ ./autogen.sh
--with-automake=/gnome/GNOME2/bin/automake-1.6 -- --prefix
/gnome/GNOME2 --enable-maintainer-mode --disable-static
--disable-gtk-doc --disable-plugin-builddir --disable-tests
+ using alternate automake in /gnome/GNOME2/bin/automake-1.6
+ options passed to configure:  --prefix /gnome/GNOME2
--enable-maintainer-mode --disable-static --disable-gtk-doc
--disable-plugin-builddir --disable-tests
+ check for build tools
  checking for autoconf >= 2.52 ... found 2.54, ok.
  checking for /gnome/GNOME2/bin/automake-1.6 >= 1.5 ... found 1.6.3, ok.
  checking for libtool >= 1.4.0 ... found 1.4.2, ok.
  checking for pkg-config >= 0.8.0 ... found 0.12.0, ok.
+ running /gnome/GNOME2/bin/aclocal-1.6 -I common/m4 -I
/gnome/GNOME2/share/aclocal...
+ not running libtoolize until libtool fix has flown downstream
+ running autoheader ...
autoheader: `config.h.in' is unchanged
+ running autoconf ...
+ running /gnome/GNOME2/bin/automake-1.6 -a -c...
configure.ac:9: your implementation of AM_INIT_AUTOMAKE comes from an
configure.ac:9: old Automake version.  You should recreate aclocal.m4
configure.ac:9: with aclocal and run automake again.
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/lang-compile.am: AMDEP does not
appear in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/depend2.am: AMDEP does not appear
in AM_CONDITIONAL
/gnome/GNOME2/share/automake-1.6/am/lang-compile.am: AMDEP does not
appear in AM_CONDITIONAL

(and that goes on and on)

basically, your aclocal is picking up old automake macros (from before
1.5) which causes the build to fail.  I can't say on your system where
these old ones are (I would guess somewhere in prefix/share/aclocal.
In any case, you might want to try pointing ACLOCAL_FLAGS (the env
var) to the location of the most current automake macros.

It's the only way to fix it if you insist on putting automake in a
different prefix - other packages that need automake >= 1.5 will have
this problem too I think.

Can I close this?