Here is how i got my Harmony Smart Control and Flirc to suspend and wake up my HTPC Linux Mint box.
Note: make sure you are connecting your Flirc to a consistently powered USB even if the PC is powered off, to choose one; power off your pc and connect your mobile on the desired USB port and make sure your mobile is charging with the box turned off.
1- Download Flirc latest Linux GUI from here (i used the zipped x64 version).
2- Add the file 51-flirc.rules to /etc/udev/rules.d/ (download the file from here), this udev rule insures that the GUI can connect to Flirc without root permissions.
3- Unplug then Plug your Flirc or restart your box for changes to take effect.
4- extract the GUI tools and run the file named Flirc(might need permissions update), you should now see the GUI and the title bar should says connected.
5- Upgrade your Flirc settings and flash it to the latest FW version using the GUI tools, from File -> Advanced, do the following:
enable sleep detection.
enable noise canceler.
enable built-in profiles
click on force FW upgrade.
6- by now, you should have no problems running XBMC with flirc and Harmony or any other remote.
7- locate two free buttons on your remote that will be used to wake and suspend your box.
8- follow the steps from 2 to 6 mentioned in this great post (Flirc will apear as 'Clay Logic').
9- Unplug then Plug your Flirc or restart your box for changes to take effect.
10- Re-lunch you GUI tool and switch to the Full keyboard view.
11- Record the wake on the remote on the Flirc virtual keyboard.
12- Record the suspend button on a combination of your choice (that does not conflict with XBMC's default map!), i used Ctrl+Del.
13- create the file ~/.xbmc/userdata/keymaps/suspend.xml with the following content (change the mapping to your preference in step 12)
<?xml version="1.0" encoding="UTF-8"?>
15- if everything went fine, you should now be able to suspend/wake your XBMC box.
16- you can expand the functionality to Gnome by adding the same shortcut to as a keyboard shortcuts to call 'sudo pm-suspend' (need to switch to sudo with no password)
17- using Harmony software i added my wake and sleep buttons to be executed when powering on/off activities or switching between them.
Hope this helps, let me know if you need more details!