I use silicon sealant to glue tiles to wood to make coasters. I have found
that if you use white spirit (turps) to clean up while the sealant is still
wet it makes a very good job. I'm sure it will work just as well on glass
but I have not tried it.

Tom

I use clear rtv silicone sealant to glue glass top goblets to wooden
stems. Works great and you can't see the sealant.
You just need to be careful and not use too much because it's
difficult to get the sealant off of the glass. I'm sure something will
take it off but it's easier not to use too much to begin with. It
takes 24 hours to cure. It sticks to the glass much better than to the
wood and you can pull it apart and all the sealant will be on the
glass. It does however make a joint that is more than adequate.
Bob
http://www.outofcontrol-woodturning.com