As someone who has seen one and only one 3D movie in the past five years, I get more use out of the 3D effect than I thought I would. I sort of go through phases with it, sometimes using it often, sometimes not at all. Now that I think about it, I've spent a lot of time playing DS games on my 3DS, which probably skews my perception of how often I use the 3D effect during 3DS games.
I guess what I'm trying to get at is that I like the 3D effect. It helps that it feels like an extra feature and not the reason I bought the system, sort of like StreetPass.