WoW64 is now implemented in wine 1.8-2, and should soon be in wine-development, too.
Wine now supports and uses shared WoW64/64-bit wineprefixes if wine, wine32 and wine64 are installed. So this should work now for all newly created default (=64-bit) prefixes and existing 64-bit prefixes. WoW64 works in Wine by - adapting the /usr/bin/wine script, - adding a /usr/bin/wineserver script that defaults to the 64-bit wineserver, and - not installing wineserver in wine's configured bindir (= libdir) (/usr/lib/*/wine/wineserver). However I assume that we have to patch the wine source to look for wine-development, wine64-development and wineserver-development in PATH. At least wineserver was found in @bindir@/wineserver up to now, which doesn't exist anymore (and would break the WoW64 setup, if both the 32-bit and 64-bit wineserver existed there). Next Wine looks in PATH for wineserver, where /usr/bin/wineserver belongs to wine (stable). See the wine and wineserver manpages. Similarily the 64-bit wineloader needs to be found (/usr/bin/wine64-development). I don't have any documentation pointers about that, but found it to be relevant.