I would say Nintendo is the one I respect the most.

They have been a game company right from the start back in 1889
They consistently innovate with hardware - analogue stick, rumble, motion control, virtual boy :P
Their software and hardware are typically high quality.

On a side note I lost my respect for Microsoft due to the blatant design and manufacturing defects on the 360 were outrageous.... real pity because the original XBOX was a fantastic system.

Nintendo because they create more value. Yes, I realize they may not create more value for you, personally, but they make a good margin on all their products which means they're adding value to the products they sell. Microsoft and Sony... not so much.

-I respect Sony for sticking it out through the tough times. When the PS3 launched, everybody was against it (including me) for some reason. Sony stood tall, ignoring the haters and releasing some damn good games along the way. They paid the price for their arrogance and are a better company because of it. Plus, my biggest gripe about Sony in the past is that their hardware was always poorly made and they relied on third parties a bit too much. The overcame both of these for me, this gen.

-I respect Microsoft because they did the impossible. The beat out Nintendo last gen and beat out Sony this gen (in sales). They took what was perceived as a hardcore brand and made it a popular console for the masses. Their strategy for gaining marketshare this gen was sound and they've provided some great services, content, and features for their fans. On top of that, they took what was a disaster (the RRoD fiasco) and overcame it with amazing customer service.

-I respect Nintendo because, when everybody was counting them out last gen and thinking that they may go third party like Sega, they shocked the world. Nintendo has always been a company that does its own thing and doesn't bend. With weaker graphics, less features, unrefined online, and poor third party support, they kicked ass and took names. -And their new 3DS is the source of so much of my gaming joy right now, it's ridiculous. I'll never doubt Nintendo, again.

As for who I respect the most--None of them. Their all money hungry corporations. Fight the power!!