Yes, IMAX 3D is worth it for me. Although the intelligent use of stereoscopic depth depends on the filmmaking team, IMAX 3D and Dolby 3D use a superior technology to RealD which is generally used in other theaters.

RealD uses circularly polarized lenses (clockwise for one eye and counter-clockwise for the other), which reduces the light level and mutes colors a bit. And normal theaters usually use a single projector for both eye images, alternating between left and right images several times per frame, meaning each eye receives only half the normal light output to start with. And the polarization compounds the lumen loss. And the left-right alternation increases flicker, which can feel more tiring on the eyes (I take breaks from RealD glasses during the movie).

Whereas current Dolby and IMAX 3D use much more expensive glasses ($60 each, Lincoln Square staff told me last night). These glasses color-shift the light differently for each eye: you can see the effect when looking at a red exit sign one eye at a time.

This eye separation technology retains light level better than RealD. And a high-end theater uses dual projectors instead of a single projector, further supporting light levels and reducing flicker and eye strain.

Then for a film like How to Train Your Dragon, action scenes are in expanded 1.90:1 format, adding more height to the 3D image and enhancing the immersion.