It seems that using , which is almost always incorrect in GMAT, and that , in which tends to be correct more often than not. Any thoughts on this Stacey?

You mean using comma which, yes? That is not almost always wrong - in fact, that is a very common (correct) grammatical structure.

If you have a choice in a particular question between "comma which" and "in which" though - then, yes, there it's more likely to be the "in which" option simply because it's a common mistake for people to use "comma which" when they should be using "in which." That's not to say the "comma which" can't be right in that setup - just that it's more often "in which" simply because of the nature of the mistake people tend to make.

So when would "in which" be used?

you'd use 'in which' when the noun following the comma would, in a rearranged version of the sentence, serve as the object of the preposition 'in'.

that's really awkward to explain in words, so i'll parley with an example:
at the end of the hallway is a large box, in which you may place the donated clothing.
the reason you use 'in which' is because this is basically another way of saying
place the donated clothing in the large box at the end of the hallway.

more examples:
i bought the olives at that grocery store --> that's the grocery store at which i bought the olives (note: you can also use 'where' here, but pay attention to the correspondence with 'at which')
phenomenon X occurs to this extent --> this is the extent to which phenomenon X occurs