The cases where it's not superior are the cases where it cannot be forced (original Halo, for example). MSAA + TrAA is superior in almost all cases. Which one is better in terms of looks is not so dependent. Which one is better in terms of performance is highly dependent on your system and the game you're playing. On newer GPUs and in newer games it is the exact opposite with FXAA being nearly free and MSAA being the killer. On older titles or older GPUs with too much RAM, MSAA is nearly free whereas FXAA is a performance killer. And where are modern gamers taxed the most? Memory bandwidth and available video memory. The problem is that MSAA + TrAA is a huge video memory and bandwidth hog, whereas FXAA taxes your shading power. Thus, MSAA + TrAA is generally better in terms of image quality. When combined with Transparency Anti-Aliasing, MSAA can offer edge-smoothing comparable to FXAA (minus some shaders), but without losing the finer details. FXAA is basically going thermonuclear in the war against jaggies. It also blurs textures, causing you to lose fine details. The problem is that if you force it in a game not designed for it, it blurs the UI/HUD and text. MSAA only hits the edges of geometry, whereas FXAA literally anti-aliases the entire screen using a shader-based method. The problem is that it's no so much subjective as it is a trade-off. FXAA, you get better sharpness with MSAA, but no anti-aliasing on shaders or alpha-textures. In terms of looks, 16xCSAA + 8xTrSSAA is far superior to FXAA. Going forward FXAA should continue to have the performance advantage over MSAA. On the newer 670/680 cards, FXAA > MSAA in performance. On mid-range cards and some older high-end cards, they can come out about even, but it's totally situation dependent. On older cards with too much RAM (I'm look at the GT430 people w/2GB RAM), MSAA > FXAA in performance. This makes FXAA nearly free whereas MSAA has a larger performance impact.
On newer cards like the 670/680 series, we didn't see a massive jump in available memory or bandwidth, but there is a ton of extra shading power. That's pretty bad that those two methods combined offer a similar performance hit as FXAA.
However, I was comparing 16xCSAA + 8xTrSSAA vs. On my GTX 560, they come out about even in tests run on WoW and Batman: AA. Enabling FXAA is near crippling while MSAA is nearly free up to 16xCSAA.
Older games on my laptop's GeForce GT130M 1GB tax the 32 shader units pretty hard. Whichever is taxed less prior to selecting your AA method will give you the better results. FXAA uses shader units whereas MSAA uses video memory and bandwidth. Anyone who tells you that FXAA offers better performance or is nearly free is sadly misinformed.