Elmer's China and Glass glue.
The best type of glue to use for bonding glass to metal is a clear epoxy adhesive.
The best glue for adhering paper to glass is a clear-drying, acid-free adhesive specifically designed for paper and glass surfaces.
A clear epoxy adhesive is typically the best type of glue for bonding glass and metal together.
The best glue for bonding paper to glass for a strong and durable bond is a clear epoxy adhesive.
The best type of glue to use for repairing a broken window glass is a clear silicone adhesive.
Epoxy or silicone will both work.
For glass, it is best to use a clear, waterproof adhesive specifically designed for glass bonding, such as a cyanoacrylate (super glue) or a silicone-based adhesive.
A clear adhesive like epoxy or silicone will work well for bonding glass to glass. Make sure to follow the manufacturer's instructions for the best results. Keep in mind that some glues may leave a slight residue or haze on the glass surface.
Elmer's Glass glue would work, but I'd recommend taping the back too.
Epoxy is best for gluing glass to wood.
The short answer is, you don't. To get truly crystal clear glue, you have to use solvents, which are toxic, or polymers which can be activated with ultra-violet light, which are also toxic. Non-toxic glues are usually based on plant starches so they are harmless if eaten, but produce glue that still has a white tint when dry.
To glue glass crystals to wine glasses a clear epoxy resin would be best, or a waterproof cyanoacrylate (most are water soluble so the crystals will come off after several washes).