Not being a virtuoso as far as this game goes, this is what I've picked up on.
You can disenchant legendary items(red items) for a CHANCE to get ruby,topaz,obsidian or zircon. A lot of the time you'll get lesser gems though.
You can realiably farm "good" gems from map lvl 500 or beyond. Map lvl 500 gives the best mix of drop quantity vs how hard the map is, as far as I know.
Farm legendary(red items) or better (green/blue) and disenchant OR get a toon to map lvl 500 and farm away.