I also had that issue with the PS3. To get around it, I purchased
this remote. It was easy to configure with the Harmony remote and works like a charm.
The only function it notably lacks is "Power On" (strange, but true). To get around this, I bought
this charger station (up to 3 controllers at once), which works great. It looks decent enough, too, so I found a place near my primary seating poisition for the controllers (within arm's reach if you're like me).
I use the Harmony remote to turn on everything else and a controller to turn on the PS3. Done.
[You could also do it without the charging station with slightly more work moving controllers around for charging the long run. I'm lazy. :P]
Hope that helps!