There is complete list of rare gems used in various skills:

• Jasper
  
  • Carpentry - Gem case
    
  • Tailoring - elven shirt, elven shirt (dark), elven pants, elven boots, hide gorget, leaf gorget
    
  • Quest for Table Saw
    
  
  
• Rubellite
  
  • Tailoring - female elven robe, hide pauldrons, hide gloves, leaf arms, leaf gloves
    
  
  
• Flame Coral
  
  • Tailoring - elven robe, hide pants, hide tunic, female hide chest armor, leaf leggings, leaf tonlet, leaf tunic, female leaf tunic
    
  
  
• Star Onyx
  
• Lapis Lazuli
  
• Aquamarine
  
• Sol Topaz
  
• Dark Sapphire
  
  • Bowcraft/Fletching - assassin's shortbow
    
  
  
• Turquoise
  
  • Bowcraft/Fletching - frozen longbow
    
  
  
• Perfect Emerald
  
  • Tinkering - pet leash
    
  • Bowcraft/Fletching - lranger's shortbow
    
  
  
• Ecru Citrine
  
  • Quest Surveyer's Scope quest
    
  
  
• Fire Ruby
  
  • Quest Surveyer's Scope quest
    
  • Bowcraft/Fletching - barbed longbow
    
  
  
• Blue Diamond
  
  • Blacksmithy - gemmed circlet
    
  • Bowcraft/Fletching - longbow of might
    
  
  
• Brilliant Amber
  
  • Bowcraft/Fletching - slayer longbow
    
  
  
• White Pearl
  
  • Inscription- t-map book
    
  • Bowcraft/Fletching - lightweight shortbow
    
  • Quest Aquarium Delights