The only gems you'll need in SoA are a diamond and a bejuril which are used to upgrade the Horn of Valhalla. You'll also need a rougue stone for the Twisted Rune plot.
Only Cromwell upgrades weapons. The exception to this is the flail of ages which you can forge yourself in Nalia's quest, and the horn which is done by Maheer in Waukeen's Promenade.
If you intend to proceed onto ToB, then be aware that gems'll come in very useful. Refer to the ToB manual of what to sell and what to keep. Off hand, from memory, items can be upgraded but will need diamonds, rogue stones, king's tears, etc.
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"Butt-kicking for goodness!" - Minsc
"Cities always teem with evil and decay. Let's give it a good shake and SEE WHAT FALLS OUT!!" - Minsc
