The native client will be able to wake your computer, provided that

1) your Mac has a wired connection to the WLAN base station your 
iPhone/iPod Touch is connected to (as you already pointed out, wake-on- 
LAN is not supported by WLAN adapters, including those built into 
Macs, as it really is an Ethernet-only feature)

2) your WLAN base station routes the wake-on-lan (WOL) packet to the 
Mac via an Ethernet connection.

This feature will f.ex. work with at least the latest AirPort Extreme 
(probably also earlier ones, but I only have access to the latest one) 
and Time Capsule base stations, but will not work with i.e. the 
AirPort Express, which does not route the WOL packet between its two 
different wired and wireless sub-networks.

Best regards, 
Felix Schwarz