When building the programs (first one it tries is ogrinfo), the link stage tries to link the .o (ie ogrinfo.o) in the source dir. But these are in .libs/ and the .lo is the one in the source dir. So, it complains about a missing .o. It looks like from the makefile (ogr/gnumakefile) nothing has changed, so maybe libtool changed to now build .lo's (libtool v1.5.2 in GDAL 1.4, now v2.1 in trunk).
(cd ogr; make apps)
/bin/sh /Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/libtool --mode=compile --tag=CXX /Users/kyngchaos/bin/c++ub -Wall -Os -Iogrsf_frmts -I. -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/port -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/gcore -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/alg -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/ogr -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/ogr/ogrsf_frmts -I/Library/Frameworks/PROJ.framework/unix/include -DPROJ_STATIC -DHAVE_GEOS=1 -I/Library/Frameworks/GEOS.framework/unix/include -DOGR_ENABLED -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/port -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Users/Shared/unix/geotiff/include -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Users/Shared/unix/netcdf -I/Users/Shared/unix/netcdf/include -I/Users/Shared/unix/cfitsio -I/Users/Shared/unix/cfitsio/include -c -o ogrinfo.o ogrinfo.cpp
libtool: compile: /Users/kyngchaos/bin/c++ub -Wall -Os -Iogrsf_frmts -I. -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/port -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/gcore -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/alg -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/ogr -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/ogr/ogrsf_frmts -I/Library/Frameworks/PROJ.framework/unix/include -DPROJ_STATIC -DHAVE_GEOS=1 -I/Library/Frameworks/GEOS.framework/unix/include -DOGR_ENABLED -I/Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/port -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Users/Shared/unix/geotiff/include -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Library/Frameworks/UnixImageIO.framework/unix -I/Library/Frameworks/UnixImageIO.framework/unix/include -I/Users/Shared/unix/netcdf -I/Users/Shared/unix/netcdf/include -I/Users/Shared/unix/cfitsio -I/Users/Shared/unix/cfitsio/include -c ogrinfo.cpp -fno-common -DPIC -o .libs/ogrinfo.o
/bin/sh /Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/libtool --mode=link /Users/kyngchaos/bin/c++ub ogrinfo.o /Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/libgdal.la -o ogrinfo
libtool: link: /Users/kyngchaos/bin/c++ub ogrinfo.o -o .libs/ogrinfo -Wl,-bind_at_load /Users/Shared/src/gdal/gdal-svn-trunk-2007.09.29/.libs/libgdal.dylib -L/Library/Frameworks/PROJ.framework/unix/lib -L/Library/Frameworks/GEOS.framework/unix/lib -L/Users/Shared/unix/expat/lib -L/Library/Frameworks/Xerces.framework/unix/lib -L/Library/Frameworks/UnixImageIO.framework/unix -L/Library/Frameworks/UnixImageIO.framework/unix/lib -L/Users/Shared/unix/hdf/lib -L/Users/Shared/unix/ogdi -L/Users/Shared/unix/ogdi/lib -L/Users/Shared/unix/geotiff/lib -L/Users/Shared/unix/netcdf -L/Users/Shared/unix/netcdf/lib -L/Users/Shared/unix/cfitsio -L/Users/Shared/unix/cfitsio/lib -L/usr/local/pgsql/lib -L/Users/Shared/unix/dap/lib -lxml2 -liconv -L/Library/Frameworks/SQLite3.framework/unix/lib -L/Users/Shared/unix/mysql/lib/mysql -L/usr/lib -lproj -lgeos -lgeos_c -liodbc -liodbcinst -lxerces-c -ljasper -lmfhdf -ldf -logdi31 -lgif -ljpeg -lgeotiff -ltiff -lpng -lcfitsio -lpq -ldl -ldap -ldapserver -ldapclient /usr/lib/libxml2.dylib /usr/lib/libiconv.dylib -lpthread -lsqlite3 -lz -lm -lssl -lcrypto
powerpc-apple-darwin8-g++-4.0.1: ogrinfo.o: No such file or directory
i686-apple-darwin8-g++-4.0.1: ogrinfo.o: No such file or directory
lipo: can't figure out the architecture type of: /var/tmp//cc3cdiTP.out
make[1]: *** [ogrinfo] Error 1
make: *** [ogr-apps] Error 2