Well, all I can say at this moment is that gear score depends on: - ilvl of your item. That number will be replaced with "real" item value at some point, but for now, item levels are taken into account - value of that specific item (trash, common, uncommon, rare, epic, legendary). If that item contains gem slots, gem quality is taken into account - resilience found on each item (resilience is useless in PvE 99% of the time, so if that specific item got its ilvl with resilience included, it should have slightly lower ilvl). Yes, I know that some PvP weapons are just as good, if not even better than some PvE items, I'll look into that problem soon. - few more factors which shouldn't have any big influence on the overall gear score
Now I'm sure I'll get flamed now for "why don't you remove penalty from .... and put penalty for ..... etc, etc" but as far as I see, this formula does the job fine most of the time. I'm not saying it wont be changed at some point, maybe even very soon, I'm just saying how it is at the moment.
I'm more interested how to figure it out in game, so that i can build a "max GS" set to log out in. At least for rogues a lot of uldar gear is still BiS(unless you are doing ToGC25). It's annoying to have pugs go "ohh you only have a 2600GS, no ToC for you". I'm curious would putting on gear for a different class that was a much higher ilvl help you "inflate" your gear score?