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.)

--- a/m4/libtool.m4
+++ b/m4/libtool.m4
@@ -2645,7 +2645,7 @@
   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`'
 m4_if([$1], [],[
   sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"])
   sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'