These are instructions that worked for my ubuntu 12.04-based XBMC HTPC.
None of the other howtos I could find actually worked for me. Recent ubuntus (e.g. 12.04 or later) use udev and automatically query the "wakeup" capability of USB devices, and allow setting the "wakeup" property of the device only if it supports it.
The "stable" FLIRC firmware does not expose the "wakeup" capability to the kernel. Only later "fw_wakeup" betas do (starting in v2 I think).
Anyhow - here is the proce