So, with my NaNoWriMo project on its fourth month, I'm finally coming to the end of the first draft. Compared to what's coming next, that was the easy part.
It's my opinion at least, that your second draft on any work is the most dangerous. Not only are you looking for things to clean up, but you're looking for things that need to be added in. Character and setting descriptions, conversations, plot details that seemed to have slipped past. If a first draft is the bare bones of a story, the second draft is putting the skeleton together, making sure it holds itself up and that everything looks right.
The best way to start is a simple read-through, from front to back. Not only is it a good morale boost to read the entire finished first draft, it allows you to pick out the easy errors: misspellings, homophones, glaring punctual and paragraphical errors. It also works as a reminder as it may have been a fair while since you last saw the first few pages.
From there, it should be much easier to see plot-holes, plot-lines which went nowhere, and things which seemingly jumped out of the blue. This shows you things to add, things to remove, and things to change.
Things to add.
Personally, I have an issue with character descriptions. I never seem to be able to slide them in during the first draft, which occasionally causes issues when I try to describe something later on. Even when it doesn't become an issue, it's nice to have a good idea of what the characters look like.
Upon re-reading a section, you might find it actually doesn't mention something you thought you had explained. In the second draft, this means going back and filling in important details that the reader needs to know which may have been left out because it was something you, (the author) knew well enough that you thought you had explained it when you really hadn't.
Adding things is probably the hardest part of a second draft. It's one of the main jobs of this revision to ensure the entire story is there, but you have to make sure you don't add something which contradicts something else later on in the story. This can be something as small as a change in a character's eye color that you then fail to switch over in every later instance, to an attempt at foreshadowing which gives away a plot twist chapters before it happens, or a bit of background on a character which drastically changes how he should react in a pivotal scene later on. Not that you should be afraid of adding things to a work after the first draft, but definitely be aware of what it can mean when you do.
Things to remove
While more of a focus for later revisions, some obvious flaws can be pulled out of the second draft. For instance, if you're aware of certain words that you have a tendency to abuse, you can keep an eye out and strike them from where they aren't needed. I have a habit towards redundancy, even to the point of using a single word two, three, or four times in a single sentence, particularly with the words "though", "before", and "often".
You should also keep an eye out for sentences which don't serve an obvious purpose. Even in a novel of 70, 80, or 120,000 words, each word should be able to carry some of its own weight. If it's not description, characterization, or action, ask yourself if a sentence really needs to be included. If not, strike it out.
Draft, the second
All that adds up to an ordeal which in some ways can be even harder than writing the first draft. I've seen it suggested that you should take a break between drafts, and it does somewhat ring true. Give your eyes and mind a break to recharge, so that you can come back later with the energy and a freshness which will allow you to read over your manuscript and spot things you may have missed otherwise. It also allows you to re-discover the story and see it better as a reader might.
It should go without saying that a book should go through several drafts and revisions before you send it out anywhere. Don't think that ten or twelve revisions means you can go without an impartial editor though. All those revisions just make it easier (and sometimes cheaper) for the editor to do their job of pointing out the things you didn't know were problems and you will always need eyes that aren't your own to look over your work. Sometimes you're just going to miss things no matter how many times you go over it.
So try not to stress too much. It's not like people are going to notice if your blonde, blue-eyed heroine suddenly turns into a black-haired, green-eyed heroin halfway through the novel anyway. Heh.