I've got a long list of favorite words and phrases; I'm sure I use them all the time when I'm talking. They pop up in all my first drafts. The short list:
needless to say
as a result
on the other hand
I think not
that (I find "that" everywhere in my drafts!)
It was fun looking through a first draft and picking out my pet words and phrases. I'm a "pantser": I blurt out everything I can think of in the first draft, globs of backstory, disconnected events, notes to myself, text in different colors where I've inserted notes about the notes about the notes. No one but me can make sense of the first draft, nor the second. It's often not until the third draft that I have a story with a beginning, middle and an end.
And punctuation. I've been known to type long passages with no punctuation so I can get an idea on paper.
But I can be blind to my pet phrases; before I send my work to an editor I search for pet phrases using the search function in Word: occasionally a page with light up with yellow highlights when I thought I'd done a terrific job of excising the devils.
Want to see more? Squidoo has a list of commonly overused words. And my favorite, Lake Superior State University's list of banished words and phrases.