Personally, I don't care for them much. Particularly when writing fiction, language style is definitely what seems natural: there isn't a 'right' and 'wrong'. I concede that style manuals are fun to look at sometimes, and there are a few things – italicisation of newspapers or song titles and so on – that my generation wasn't taught at school.
Here are a couple of examples. Some people just hate semi-colons (a word that can be spelled without the hyphen, of course). A semi-colon should separate two linked sentences; the two sentences should be independently viable but feel better connected.
Another bad boy is the "comma splice", sometimes known as the "comma fault". Occasionally it feels right to separate two sections with a comma, the words just read better that way. But you can't lay down rules for any of this. (That comma could even be a semi-colon, for instance. Or just two sentences. Or a dash.)
To quote Lynne Truss (not the Tory cheese woman), "done knowingly by an established writer, the comma splice is effective, poetic, dashing." I'd suggest the rest of us should consider dashing.
Finally, it so happens I completely disagree with Grammar Girl on the use of commas – I just happen to think she's coming from completely the wrong angles. The use of a comma is generally easy for me: it's where you stop to breathe. Just about everyone of my generation would agree with me.
That doesn't mean she's wrong, though, it just means that her style and mine are different...