In Gentoo Prefix we go by Apple's convention to give modules the .bundle
extension.
http://developer.apple.com/documentation/DeveloperTools/Conceptual/XcodeBuildSystem/500-Linking/bs_linking.html
(Above link was removed by Apple, the link below contains a copy:
http://disanji.net/iOS_Doc/#documentation/DeveloperTools/Conceptual/XcodeBuildSystem/500-Linking/bs_linking.html,
in case it disappears also, the relevant quote:

Bundle. Bundles are executable files that can be loaded at runtime by
other products. Plug-ins are implemented using bundles. The term bundle
in this context refers to the binary itself, not to a structured
hierarchy. Bundles have the .bundle extension; for example,
MyBundle.bundle.)

--- configure
+++ configure
@@ -12172,11 +12172,11 @@
   version_type=darwin
   need_lib_prefix=no
   need_version=no
-  library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+  library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext'
   soname_spec='${libname}${release}${major}$shared_ext'
   shlibpath_overrides_runpath=yes
   shlibpath_var=DYLD_LIBRARY_PATH
-  shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+  shrext_cmds='`test .$module = .yes && echo .bundle || echo .dylib`'
 
   sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"
   sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'