I learned how to write in junior high and high school.  Years of repetitive English classes drilled rules and patterns into my head.  But there were a few things I was never comfortable with, so I break some major rules pretty often: 

1.  Prepositions ending sentences.  "Prepositions:  What are they good for?" is a perfect example of why I don't like that rule.  I speak this way in normal, everyday conversation, so prepositions will appear at the ends of sentences in my writing. 

2.  Commas separating groups of things.  There should be a comma before the "and" if you have a first thing, a second thing, and a third thing.  The rules say it can be done either way; I think it's either my way or the wrong way. 

3.  Punctuation within quotations.  Did I say, "Shut up?"  Or did I say, "Shut up"?  I think I said the latter, and even though it breaks major punctuation/grammar rules, that's the way I do it.  I also might use punctuation in the quotation and outside as well:  I used to say, "Shut up jerks!".