I hope the issue I raise here is of interest for many other people, maybe it was already solved...
I am able now to shut down the HTPC using the Hauppauge remote supplied with Nova-T 500 HD card, without impairing the functionality in any way. It was easier than I thought, plenty of info around.
Is there a way to have the pc starting up using the same remote? One way would be to build a basic IR receiver and install the terminals in parallel with the on/off button. This system would need power to receive the signal, so I will have to find +5V somewhere even when the pc is in "power off" mode. If this is not an option, maybe a battery can be used to power this device? You need +2.4V to +5V, not necessarily 5V, so maybe 2x 1.5 batteries would do the trick?
But I would like to minimise modifications on the wiring connected to the mobo...

Something based on this idea: http://www.instructables.com/id/Universal-IR-Remote-Switch/ , of course without the relay and all the other bits... or maybe the relay will just keep everything away from the mobo... will give me the "clean contacts" I need...
What would be the most elegant / solution?
i heard about some remote controls, like the one supplied with Windows MCE, able to do that. Not really interested, as I could get two good silent fans for the same money (TBH, I am more in need of those than the remote control...)