Decision to change how damage bonuses of the new and improved Rubies are calculated, was a good one too, it's transparent and clearly understandable now, though those numbers are a bit low. Re-evaluating the numbers on the Rubies before 1.0.7 ships is a key here, since Emeralds are a clear choice now. Please focus more on this, because "Radiant Star Ruby: +120 minimum damage/+120 maximum damage (up from +20/+20)" is really not comparable to Radiant Star Emerald bonus.
Regarding Topaz and Amethyst:
Change to Topaz damage (Weapon: Melee attackers take 2500 per hit) isn't a solution to the problem. Thorns and Topaz values should be a % of the incoming damage instead, this is how it has always worked in Diablo games. That will work both in inferno and normal diffuculty, current properties aren't.
We'd also suggest to bring diversity by changing Amethyst properties when socketed to weapons from Life on Hit, to much more desirable Life Steal - you will lose dmg bonus provided by Rubies and Emeralds, but you'll gain much needed surviveability. Since the game is around for a while, no one will invest in current, such low values of Life on Hit. It could look something like this:
Radiant Square Amethyst: 1.50% of Damage Dealt Is Converted to Life
Star Amethyst: 1.70% of Damage Dealt Is Converted to Life
Flawless Star Amethyst: 1.90% of Damage Dealt Is Converted to Life
Perfect Star Amethyst: 2.10% of Damage Dealt Is Converted to Life
Radiant Star Amethyst: 2.30% of Damage Dealt Is Converted to Life
Marquise Star Amethyst: 2.50% of Damage Dealt Is Converted to Life