Yes, always. In any game or app. I don't see why not.
It vastly improves graphics because of the added depth. (Glassesless) 3D over higher resolution any day. Luigi's Mansion is probably the best to date, each room looks like a small diorama. It's very pretty and what LM should've been on GameCube. Also, more importantly, it helps greatly in gameplay because you tell distances in for example platformers extremely easily and naturally. In Mario Kart 7 it helps to. I'm way better able to predict the path of a fellow racer, which I'm a way better aim with shells than I would be on a console. In fact, I notice that I got spoiled by this ease on the 3DS and even begin to have trouble predicting these things in console games. There's really only pro's and I hope the feature remains in Nintendo's handheld successor.
The headaches and the sweetspot are nothing but excuses to me. Especially that last thing, it's not like you have to hold your head perfectly still and in the dead center. You can actually move around quite a bit. Moreover, it is even possible to comfortably have 3D on while someone else is watching if they're close enough. I don't get what's there to get headaches from either, it's already been proven the effect does not damage your eyes or anything. I don't even have good eyes, but they adjust to the dual image for a seemless 3D picture in less than a second. I will admit that if you use the technology for the very first time your brain and your eyes have to learn how to deal with it, I noticed my eyes adapting faster and faster the more I used it. Maybe the same is true if you only use it sporadically I don't know.
EDIT: And spurge... You broke the thread
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