Let’s list often confused terms. Terms that are spelled or sound the same, and are for that reason inadvertently confused.
Mine:
The possessive pronoun its and the contraction it’s are confused to the point that its no longer seems to exist. My iPad autocorrects its to it’s, regardless of context, and the smartest people in the world, i.e., Dopers, get it wrong most of the time. That includes the OP. 
Doesn’t the agricultural term mean no pesticides were used in its production?
I should bloody well hope that’s the case for ALL bottled water on the market
You’re right, words mean what the people who use them mean by it. I do have some difficulty seeing how a bottle of water can be organically grown, though, so I’m rather curious to find out what people actually mean when they say that a bottle of water is organic. I mean, the least organic thing about a bottle of water seems to me that it includes a bottle, which is hard to escape from in the business of water bottle production.
Edit: Like Aspidistra said. Didn’t yet see his or her comment there.
Inflammable, and flammable:
Does anyone know what’s the straight dope with the incorrect spelling “rediculous”? I see this all the time now on the Internet instead of the correct “ridiculous”.
Is this a meme, or some kind of ironic spelling? I can’t understand why people would be making the same simple mistake so frequently, when spell-checking software is so common.
My contribution:
Reflection and refraction.
Reflection is the tiny spot of light on a water droplet as sun rays hit it and bounce off again into your eye. Refraction is the fact that the droplet deforms the image of what’s behind it as light rays coming from behind change their course as they penetrate the water.
Insure and ensure.
pore and pour, mute and moot… in fact any confused homonyms that find their way into supposedly professionally edited fiction drive me crazy. It’s okay to me if the writer doesn’t know the difference. His job is telling a story. It’s wrong if the copy editor doesn’t know, though. It’s even worse if the copy editor is letting his spellcheck software do his job for him.
The Penguin Dictionary of Confusibles by Adrian Room is chock-full of such things. I have a copy here at my desk that I’ll sometimes pull down and flip through. Unfortunately, I think it’s out of print.
Obligatory: there, their, and they’re. There are two horses on their farm and they’re both mares.
Use and utilize: When you use something, you are employing its intended function. When you utilize something, you are repurposing it for a function other than that which it was designed. For example, you use a desk calculator to add two numbers. You utilize a desk calculator to swat a fly.
Herbalism =/= Homeopathy
:eek: NOOOOOOOOOOOOOO!
I suggest you take your iPad in and exchange it for one that isn’t defective.
I suspect it’s because “re-” is such a common prefix. But yeah, people who do this should be ridiculed; and if they do it again, they should be reridiculed.
Definately.
Which often gets spell-checked into “defiantly” and makes me think I’m going to loose my mind.
carom - to ricochet
careen - to tilt
career - to move fast
Shit and shinola.
Ironic and funny. Seems people are using “ironic” more and more for any situation that is amusing.
effect and affect.
It’s a reference to the Red Iculous, a Brazillian reptilian marsupial from Indonesia.
Affect - a verb. To make a difference in something.
Effect - a noun. The consequence of some action.
Technically, “effect” is used as a verb sometimes, but I consider that business-speak and undesirable.
loose and lose 
breaks and brakes
To be fair, I’m writing on an iPod and don’t always notice when I’m incorrectly auto corrected 