Ah we have the same taste in games :)

I originally asked because for most of the games I've played (and the ones you mention) the overall story played out the same regardless of your choices.

There could be branches and dialog changes but they always reconverged at important story points that stayed constant. And of course the cutscenes at very end would be different. Take DeusEx - some minor things would be different depending on your actions, and at the end you basically got to press a button to choose your ending.

The only real exception I can think of is Fallout New Vegas, where the game storyline would become wildly different as you chose to help different factions....that game was a rare exemplar of "choices matter".