just took a few hours reading the whole thread and some of the links and played around with spread sheet. There were some solid mechanics already revealed so we could predict better ways of combining gems instead of blindly experimenting.
some very important numbers were revealed in http://www.reddit.com/r/Gemcraft/comments/2385eg/sc_about_gem_combining_mechanics_and_why_we//ppAs
Combining two gems of the same grade:
Mana gain: 0.88A + 0.5B
A is the max stat (e.g. here we are interested in mana gain) of the two gems and B is the min stat. this is a very simple equation and obviously explains why the spec method gives higher stats. for normal upgrade min and max are always the same and also equal to average, since the same gem combines with itself. The spec however method exploits the fact the upgrade equation do not use the average but an unequal weights of min and max. so by increasing the max (3/4o 1/4b) and lowering the min (1/4o 3/4b) the resulting stat is higher.
here is whats interesting, the tier 4 spec dual color is optimal, since the only other 2 ways of getting to t4 (0/4 + 4/4 and 2/4 +2/4) are not as good. but the t6 spec is already not optimal as is shown in the spreadsheet below:
grade 1 pure is assigned special = 1 for simplicity sake
red box shows process of making of t4 spec, t2 o/b dual combine with t2 pure o, t2 o/b dual combine with t2 pure b, resulting in two t3 with different stats. (understand this bit and you'll understand the whole sheet)
green number shows difference between spec t6 and optimal t6)
here are ingame screenshots of spec t6 and optimal t6:
as you can see the optimall t6 is made by combining 2x spec t4 with 7/8o and 1/8o t4's.
i also tested some T8 gems, left is normal spec t8, middle is optimal t6 spec'ed into t8, right is (i think optimal t8) where 2x optimal t6 are combined with 15/16o t6 and 1/16o t6.
However this whole thing is recursive and will get exponentially more complex. e,g, for t10 you will need to combine optimal t8 with a 1/32o t8, which is in terms of grade1 gems is 4o+252b, so you start with 4o+4b t4, then combine with pure t4, t5, t6, t7 o's in order. but hang on 4o+4b tier4 is better the spec method than normal so you will have to start with spec t4. for t12 you will have to start with spec t6 but hang on spec t6 is not optimal so you start with optimal t6. it will get impossible at higher levels unless some sort of algorithm is found (e.g. you duplicate certain optimal lower tiers and save for later) but at least its pretty easy start with a better t10 and that doesn't take so long
also i only played around briefly some could look deeper into it, there are formulas for super gems as well, e.g. for mana gain its
Combining grade N gem and grade N - 1 gem
Mana gain: 0.89A + 0.44B
maybe some1 could do some maths work out the some tipping point between the different methods of combing gems
also this whole post applies for 50/50 gems only, obviously with the arbitrary numbers in the game mechanics 50/50 isnt gonna be the optimal ratio (although its easiest to upgrade, which is why spec is very good for casual/hardcore, but for real hardcore it isnt enough :P)
wow that was a big wall lol