I found a small workaround for it, but it requires having another mac in the network.
I am on a similar setup. Airport Extreme Base station in one room where the modem is and another AEBS in another room where the computers are. The two base stations connect to each other wirelessly, but the computers all all being served by the same Base station and are all wired via Ethernet.
I noticed I cannot WoL using Logmein, so I kept one of the computers (2011 mac mini) on "never sleep". I connected through logmein to it and used Apple remote Desktop to try and Wake the other. It fails.
Now the weird bit: from the Finder, you can still see the other computer (2011 iMac) in the network so I tried to connect to it. It will fail in a bizarre way: it allows me to see the first level of network shares, but won't allow me to browse further. I think this has to do with some network caching, but after retrying to wake the iMac from ARD, it succeeded.
I tried the same technique a few times under the same conditions (imac inaccessible at first, try to wake from ARD, fails, try to wake from Finder, fails, retry from ARD, succeeds).
Guess there's a big bug with WoL on ML (I'm using 10.8.2 with the supplemental update).
Apple, it would be great if you could fix it!!