You're actually looking at several different options. First of all, most games support at least 5.1 surround output, meant for home cinemas, but also used for Dolby Headphone. Take a look at this list: http://satsun.org/audio/
Regarding SBX/THX, this is another option for simulating surround. When using these, you want to have your game in headphone mode, with 2-channel output. The SBX/THX software does the rest.
Regarding games "encoded to use 3D surround on a headphone" this is something that certain games do attempt, but not many. I'm only aware of a couple. In BF3, you use their 3D simulation encoding by using headphone mode and checking "use enhanced stereo." Dirt Showdown also has their own 3D simulation encoding called Rapture3D.
I've tried all 3 of the above mentioned options and prefer 5.1 output with Dolby Headphone for positioning. Oh, and BTW, trying to combine any of these doesn't work well. It makes things sound really strange and positioning is pretty much lost.
Edit: I just read benbenkr's assessment and should add that I've only ever used Dolby Headphone with what he describes as optimal headphones: "open headphones with decent soundstage and some possess at least some tight bass." So the kind of headphones you're using might be an influence as to which technology you go with. Also, another thing to keep in mind is that the older the sound card, the more likely you will have issues with the driver. The two Xonar cards I tried both caused driver crashes, only fixed by using the unified driver developed by a third-party. If you read reviews of older cards on newer systems, you'll see lots of reports of issues. The drivers are not continually updated.