From the DA:O Wiki:
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What the game calls "middle gems", which includes Sapphires, Topaz, Amethysts, and Malachites, can be turned in to help your allies after you've finished part of the story.
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They also mention that 10 garnets will be used in a quest, so I'm saving them.
From what I can tell, things like rings w/o properties and engraved bowls, jewelry are also just for selling (unless it's labeled as a gift). Same with private documents and blank vellum.
Anyone know of other items that don't have a use other than converting to $?