Most gems that can proc on fortune are best fortuned because gregtechs implosion compressor will reduce the amount you effectively gain. Personally I don't need anywhere near as many diamonds as diamond dust so fortune is just more convenient as well.
I'd always use the grinder on Diamond or Ruby. Other gems are more of a question. Because of Coal->Diamond, and the use of Diamond dust in some recipes - notably glass fiber cable and iridium plate, you should never convert diamond dust to whole diamonds. Rubies, at some points in the tech tree, are more useful as dusts than whole due to what they centrifuge into. Unless you do a lot less mining than I did, you should never run out of whole rubies. Plus grinding ruby ore gives red garnet dust as a bonus.
Sapphire ores are still clear wins to be used in an industrial grinder. You get one whole gem, plus 1.5 in dust. 4 dusts can be turned into 3 gems. So 8 ores silktouched and ground are 17 gems. 8 ores fortune 3'd are somewhere between 16 and 20. But the grinder also gives an extra 2x tiny dust in green sapphire, which itself can be electrolyzed to normal sapphire. So total return on 8 ores is 20 gems. (The 17 from above, plus 16x Tiny Green Sapphire Dust == 4x Dust == 3x Gem) consistently, with none of the randomness of Fortune III
Green Sapphire Ore is similar because it gives 1 gem + 1.5 dust + 0.5 blue sapphire dust, again equating to 20 gems for 8 ores.
The only serious argument to be had is with Emerald. The bonus dust from the grinder is Olivine, which serves no current purpose.
Note that all of this comment is about the Industrial Grinder, only available if GregTech is available, and not what the original question was asking.