Minecraft: the game has a ton of depth, but you're very free to discover it at your own pace (especially if you start with it set to peaceful). On top of that, it's something you can play together. Note that I'd highly recommend letting her play it herself for a while before playing together so you can avoid the temptation to be a backseat driver for her (lose-lose: if you do it, you'll be annoying and put her off of the whole thing and if you don't, seeing her do newby things and saying nothing will eat away at your soul).
I'd recommend rather strongly against Dwarf Fortress. The graphics alone are a harder sell for someone not already into gaming. On top of that, the game tends to be rather brutal whereas Minecraft is pretty tranquil even with monsters on. And it goes on perpetually, whereas DF is the sort of game where you keep playing until you lose and have to start over, which frustrates a lot of people.
Edit: Someone brought up TF2 and that's also a really nice idea. It's cartoony, there are a few classes that are easy enough to learn quickly, and the game's basic mechanics are relatively east to learn. It's a good way to get used to the WASD+mouse controls found in a lot of PC games.
I was also going to say Grim Fandango, but thought better of it because a lot of those old adventure games can be maddening if you don't have experience with adventure game logic ("why on earth would I pick that up let alone combine it with this"). Great games, but not great first games. And Grim Fandango's movement controls alone are a nightmare.
