What I do to troubleshoot wake on lan:

First try to wake the machine from an S3 state.
S3 is when the machine is in sleep or standby
for machine states look here

http://software.intel.com/en-us/blog...-states-s0-s5/

If this works then it means the N900 is sending the magic packet and the network is setup properly. Then turn the machine off. Try to get it to work from S5. If you see it doesn't work check to see if the RJ45 jack on your PC has an LED it should remain on when the PC is in S5. If it isn't check your bios settings to enable wake on lan from S5. Any further steps depend on your OS. If you multiboot your PC then you also need to make sure both have wake from S5 enabled otherwise booting the OS which has it disabled then shutting down would mean it is disabled again until you boot the other OS.

If you suspect it's the app (which i doubt) then try this python script
http://talk.maemo.org/showthread.php?t=38785