I own a Kikuichi TKC gyuto (semi-stainless), and there must have been some moisture in the saya I stored it in as there were a few small rust spots on it when I pulled it out the other day. I have no experience cleaning rust off knives and am wondering what the is the best course of action?
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A standard pencil eraser does a good job on small spots. If you need more you can try some toothpaste on a papertowel. If you need more polishing power, Flitz is good or a simichrome/semichrome polish. agrussell.com sells simichrome and has a special 'eraser' just for rust. Flitz is sold at most stores with a good gun selection or online at lots of places.
Korin sells a "rust eraser" -- basically a block of felt with some abrasives in it. I somewhat think you can do the same with some slurry worked up on a waterstone on a rag.
You could also grind it out -- a sh*tload of work that requires that you put your own polish on the blade after. Then again you might have to do that in any case if you used anything harsher than a pencil eraser.
A Scotch-Brite with baking soda is enough to get rid of new rust spots. BKF has oxalic acid and unless you neutralize it -- as kmr54 describes -- it will stain your knife.
Speaking of stains, you may want to consider forcing a patina.