Yes, you can sell them all after the Twisted Rune encounter. The only other everyday gems which have a purpose are diamonds and bejurils.
Spoiler
.
.
.
.
.
.
.
.
The horn of Valhala can be upgraded with firstly a diamond and then a bejuril, by the merchant in Athkatla below the Art dealer in the market.
------------------
Never accept an invitation from Wolfgir to a BBQ!
[This message has been edited by Stealthy (edited 03-10-2001).]