After messing around with different kernels on Debian Lenny, I noticed that my system did no longer respond to WOL packets. The system is using an on-board Realtek R8168 chip which supports wake on lan.
After searching and reading i found the problem. The system is using an r8168 chip, but the driver that is loaded by Linux is the r8169 driver. If the r8168 driver is loaded, as it should be, then WOL is working again.
See also this information.
The trick is to blacklist the r8169 module. To do so, edit the /etc/moprobe.d/blacklist file and add a line reading 'blacklist r8169'
To make this permanent, issue the following commands as root or with sudo:
mkinitramfs -o /boot/initrd.img-$(uname -r) $(uname -r)
After a reboot, wake on lan should be working again.