My biggest pet peeves have probably been echoed in this thread already:

their, there, and they're
you're and your

I took a class in school that taught me the difference between words like "lying" vs "laying" (for writing in medical charts, which is a LEGAL DOCUMENT, and it just makes you look sloppy when you mix words like that up), but I do forget sometimes. I'd like to think I look like I'm a little educated though when I do speak/type as compared to many others.... granted, these smart phones nowadays sure can make you look dumb with their auto corrects...