FXAA is a post process way to antialias and is more resource intensive it seems. I tried enabling it and it mostly halved my frame rate and didn't provide much of a visual difference if any. FSAA wasn't providing much of a visual difference either on my PC with nvidia card by the way but it didn't halve the frame rate like FXAA did. I would like it if they would have included MLAA as well as that's also a post process way of antialiasing that gives you the look of somewhere between 4 and 8x MSAA yet with little to no performance penalty... although there's drawbacks to that too.
There are two major post process AA techniques right now FXAA and MLAA. Which is faster depends on what platform you are on though I read. But yeah, post process AA methods. Also FXAA is more of an nvidia backed thing and MLAA is more ATI although like I noted above FXAA halved my frame rate in DNF on my PC with nvidia so I went with FSAA as that's the only other choice there.... and MLAA isn't a choice obviously. I tried overriding the settings to enable MSAA instead but it caused major glitches with the game. So yeah.. I wended up going with FSAA.
The FSAA in Duke4 seems to be of the edge antialiasing variety that's a quick and dirty "slightly blur the edges" type of AA (but like I noted I didn't seem to notice a big difference in visuals or performance in practice). FXAA is applied to the image after the scene is rendered and does the entire scene but again seems to be heavy on the hardware. But I suggest you give both a try and see which one works better for you.
Here's an article about FXAA:
http://timothylottes...vidia-fxaa.html
This one is about MLAA:
http://www.iryoku.com/mlaa/