Please feel free to add to the list. Here's some of the ones I see all the time that the spell checker will ignore:

To, Too, Two

To - used as a preposition or as part of a verb phrase. I went to her house. I want to eat dinner soon.
Too - means "also," or "as well." I?d like to eat, too.
Two - the number, more than one, less than three. I want two pancakes.

Goldilocks went to the table to eat the porridge, but two of the bowls of porridge were the wrong temperature so after she ate, she washed the bowl she'd eaten from, dumped out the porridge from the other bowls, and washed them, too.

Affect, Effect

Affect - to modify, to pretend, or to take on. His coughing affected my concentration. I affected a glamorous pose.
Effect - a result. His coughing had an effect on me.

The years of heavy smoking affected the wolf so badly that all his huffs and puffs had no effect on the little pig's house.

Their, There, They're

Their - possessive, owned by two or more people. That is their pen.
There - location. The pen is over there.
They're - contraction for "they are" or "they were." They're not at work today.

Poor, Hansel and Gretel - they're still trying to lose those 40 pounds after their trip to the wicked witch's gingerbread house over there.

Your, You're

Your - possessive, owned by "you." Is this your idea?
You're - contraction for "you are" or "you were." You're cute when you're angry.

You're sure you can click your heels three times and get back home?

Accept, Except

Accept - to approve, take on, or be resigned to. I accept the fact that chocolate is not health food.
Except - used to single something out. I love all types of chocolate except white chocolate.

Snow White accepted all the chores given to her by the seven dwarves except for picking up their dirty underwear.