So... four years down the road, are Dragon Age (Origins) and Skyrim still the best options if you enjoy games that include nudity, but still have a good story? If so, that's kind of sad. But perhaps it's just that I'm too busy to play games these days?

I do enjoy The Last Sovereign, which is an impressive game, without having impressive graphics. I've played Corruption of Champions, My Very Own Lith, XXXivilization and a couple of others, none of which feature stunning graphics. Surely there must be something else out there?

I like the game while nude?

Dragon Age - Origins (PC Version)

You can install game mods that overwrite the texture maps of the main characters. You can then choose your character, male or female, and their relative endowments. I love playing the game with my characters fully nude. The player models are anatomically correct, fully detailed, and mouthwatering gorgeous!
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Of course the drawback to playing with fully nude characters is that since they aren't wearing any body armor, they are subject to an ass kicking by boss level creatures.

Good of War had some nudity

Skyrim with nude patch!

Heavy Rain is also a good one to check out.

Mass Effect is a good one to check out.