Well, the 3D side of things are completely independent of the display space. The only connection between the two are matrices, more importantly, the projection matrix. So that means the aspect ratio is usually defined by the projection matrix.

Now, to accomodate different aspect ratios, you could choose from several methids. One trick is to keep the vertical FOV (field of view) constant, and only change the horizontal FOV. Other method keeps the horizontal fixed and changes the vertical one. Or you could also use some combination of both.

Your real problem is the display resolution vs. the display aspect ratio. For example, the graphics card may expose a bunch of display resolutions with 4:3 aspect ratios, even though the display itself is 16:9 or 16:10. The reverse may also be true. By looking at the display mode list, there is no reliable way to know what physical aspect ratio the display uses, unless you do some OS specific queries about the display hardware and its native resolution. Even then, such info may not be available.

I guess your "fail safe" option is to allow your users to explicity chage the projection matrix aspect ratio, if needed.