Here is a list of some that most authors need to add to a quick check before publishing (Partly because they're used a lot and often skipped over.) (Do a ctrl+F and enter these in to verify you are using the word you want!)
To - Two - Too
Their - There - They're
Your - You're (A personal detriment my editor catches this one ALL the time!)
Witch - Which
Plain - Plane
Site - Sight - Cite
Hear - Here
Weather - Whether
Accept - Except
Its - It's
Some you may not even have known and might be using wrong: (These are NASTY!)
Compliment: expression of admiration verb or offering an expression of admiration
Complement: something that completes, finishes, or enhances something else or something that goes well together (peanut butter complements jelly for example)
Effect: Almost always a noun or thing - the Greenhouse Effect. If you can put a the or an in front of it, then it should be effect. The effects of his illness make him grumpy. The tip in the article below is The has an "e," e = effect.
Affect: Almost always an action, something affects something else, His anger affected her attitude. The tip I read about it was a=action, a=affect.
For several great articles on knowing the difference between homophones go here.