I just installed tomato-K26USB-1.27.9047MIPSR2-beta16-vpn3.6 on my Asus RT16, and WOL is not working for me either. Worked fine with my previous DD-WRT firmware.
I have 3 routers:
1 x RT16 - WAN router - tomato-K26USB-1.27.9047MIPSR2-beta16-vpn3.6
2 x WL-500W - Wireless client bridges - tomato-K26USB-1.27.9047MIPSR1-beta16-Ext
PC I want to wake is connected to one of the WL-500W's. I'm trying to wake it from the RT16, since that is the one I would SSH tunnel into all the time, so browser would be local login to it. This setup works in DD-WRT.
As a test, I logged into the WL-500W that is connected to the PC I want to wake, and was able to wake up it up.
I then logged into the other WL-500W (not connected to the PC I want to wake), and wasn't able to wake up the computer.
So it looks like the magic packets aren't broadcasting over the network correctly, and only seem to work for the routers physically connected to the computer you want to wake.