Personally, I stick with cyanoacrylate-based super glue. Several reasons for this.
First, combining the green and white portions of the putty (which is required to generate the adhesive property) is an exothermic reaction, and thud generates quite a bit of heat. You'll notice this as you mix it. I've heard legend of nearby coral being upset/damaged by the radiant heat of curing in the tank. Next, it does have an off-putting smell, as mentioned above. No, it is not toxic, however. Lastly, I find that the putty just doesn't stick well, particularly to maricultured liverock that is covered in various 'stuff.'
The cyanoacrylate doesn't really have any of these problems. My personal favorite as of late is the purple-colored 'reef glue' for sale online or at most decent LFS.
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