controublebrought up troublesome words in comments, specifically citing word pairs such as then/than and effect/affect. That made me think of effluent/affluent, principle/principal, capital/capitol, nickel/nickle, etc... These are troublesome not because of the homophony itself (most people don't get bare and bear mixed up, I think) but because of the overlapping or similar meanings confused with the homophony.*
What's your most/least favorite word pair?
* ETA Ok, "effluent" and "affluent" aren't really that similar in meaning. I just think it's a funny pair.