Which vs. That
Let's start with the which/that conundrum. For some reason far too many writers think "which" just sounds better. So they use "which" interchangeably with "that" and in so doing, punctuate incorrectly as well. To put it simply without all the grammar jargon, "that" introduces an essential clause and "which" introduces a non-essential clause.
"The tree that John is planning to cut down is a maple." In that sentence the tree John is planning to cut down specifies which tree the writer is talking about.
"John is planning to cut down a tree, which is a maple." In this case the tree John is planning to cut down just happens to be a maple, which is nice to know, but not necessary.
A good test of whether you should use "which" or "that" is whether the clause could be set off in parentheses or by an em-dash.
E.g., You could write, "John is planning to cut down (a maple) tree."
Or "John is planning to cut down a tree––a maple."
You wouldn't write, "The tree (John is planning to cut down) is a maple." There is no point to those parentheses.
Which Takes a Comma
Which brings me to my next point. "Which" takes a comma before it, and "that" does not. Most writers know the part about "that" and rarely make the mistake, but more and more often, I see no comma before which. When which is used correctly, there is a comma before it and at the end of the clause if it comes in the middle of the sentence. Why? Because the clause it introduces is non-essential––an aside–-so the commas function like parentheses or an em-dash. When writers use "which" when they should use "that" and don't set off the clause with commas, they are both right and wrong. Right because the clause is essential and should not be enclosed by commas; wrong because "which" cannot introduce an essential clause.
Which Brings Me to the Overuse of That
Take the above example for the use of "that" and remove it.
"The tree John is planning to cut down is a maple."The sentence still makes perfect sense.
"The gas Mary is pumping into her car is premium and costs more."Sometimes "that" just sounds a little better, especially in very short sentences with the same pronoun coming before and after the verb.
"He said that he loved me."
"He said he loved me."While they can mean pretty much the same thing, the first one flows better, because "he said he" comes off as clunky unless it's everyday speech. However, particularly in nonfiction articles, even the best writers can use "that" to death. It will occur over and over, not just in the same paragraph, but in the same sentence. I can't tell you how many times removing a "that" here and there has been enough to whittle a wordy piece down to maximum word count.
So next time you are reviewing a submission be careful of which place you use which and which place you use that, and, while you're at it, use that sparingly.