I'm not sure if you had this in school, but my English text book had lessons on words that were commonly misused and confused. Actually it had whole units committed to this, complete with a glossary.
The mentor workshops at the writer's conference covered this briefly. Here's a few words that they threw out there:
Affect/ Effect (I missed this throughout a whole essay once, but I found a trick Affect is normally the verb form while effect is the noun form, so affect = action: they both begin with a.)
They're/ There/ Their
Advise/ Advice (advise is normally the verb, advice the noun)
Its/ It's (I have to reword my sentence and extract all the contractions to spot this one.)
Words I always mix up are lose/ loose, chose/ choose/ choice, and I am forever writing what for want and want for what. Thank God for editing.
What about you? Are there words you commonly confuse in your writing?