At most it is used as a background or space for props and architecture - that cannot be interacted or used at all, as a gameplay relevant feature.
Some games did touch it, is some limited ways. Thief and such similar sneakers come to mind first.
The ability to climb to a second floor up the stairs and then shoot trough a window in other first person shooters isnt really what im talking about here.
Not even Skyrim, which is fully open 3D world enables the player to use verticality of the environment, except in some rare places where the player himself can basically cheat by jumping or falling onto some high vantage point and then use it to your advantage.
And its not that kind of games we are talking about here, in the first place.
The RPGs we do like, got it the worst.
We are forever grounded on a flat 2D surface where any sort of angle (oblique or isometric or top down or whatever), or additional 3D vertical dimension. that is there ... is there just for the show. A background.
Its not actually a part of environment. Its not something we get to actively use or even explore.
Let alone a part of the gameplay, except in some rare extremely limited or linear ways.
I would very much like to see Wasteland 2 take this opportunity and kick ass in this, so far so underused, dimension too.
Look at that art piece of rangers standing down on the street, casting their long shadows amongst the tall, overgrown with vegetation, skyscrapers. Look at the illustration of Scorpitron ...
Wouldnt it be great if we could climb onto those skyscrapers in places (not everywhere of course since you cant just climb everywhere)? Wouldnt it be great to traverse old ruined cities over those skyscrapers, finding hidden communities on top of or inside them, connected by cables and overgrown shanty bridges and vines?
Wouldnt it be terrifying to see a Scorpitron following you up one, or crawling down onto you from one? Or shooting at you from way high up there?
Wouldnt it be better to find hidden bases with vertical interiors that are all part of one big active map, so you can use the vertical dimension and height it provides in entirety? With enemies chasing you up and down or you finding an advantage over them like that?
Wouldnt it be great to be able to explore and reach hard to find places like that? By climbing or grappling your way up or down?
Or an old western looking city whose rooftops would be at your reach, to explore, or to have rooftop fights on?
The trees, hills, old tankers or battle ships and airplane carriers, truck husks, ruined buildings or houses, ... whathave you.
One small game that is isometric, completely 3D and very vertically enabled in parts, that i liked very much, was the recent Lara Croft and the Guardian of light.
Take a look at a part of it:
http://www.youtube.com/watch?v=OQYHIJbVaYU
There are other maps that are even more vertical, like these screenshots show:




The pics where you see the big inside of some temple are basically big maps that are all one big piece.
There are no loading screens or such mechanics to traverse them.
You can freely go up and down and often have to use the verticality to open some passage or solve a puzzle.
Of course, this is an adventure game and so limited to that kind of gameplay.
Wasteland 2 could do much, much more.
-edited for spelling etc -