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All my funnels have a little hole on them, either put there by the manufacturer or by me. I hang them on a wall in my garage witah a drip tray under them, that way they can drain and not get all over everything.
I use a piece of rain gutter and screw a piece of plywood over the open side(using gutter screws). The plywood has hole drilled for my funnels and the gutter runs into a oil bucket.
The long neck funnel for transmission fluid is just used occassionally and is bagged in plastic with an absorbent paper towel in the throat...and thrown on an upper shelf, out of the way. A similar funnel for gasoline transfer is bagged and tossed up also. The other smaller ones are stacked inside a 3 lb coffee can with some paper towel in the bottom. Depending on what I'm doing, I'll wipe those out real good before I use them.
I must be a clean freak to some extent. I rinse my used funnels out with gas and then dry them off and out, then store them up side down on a dish towel that I stole from work. Also I stuff a paper towel in the neck to keep out grit, and absorb any wet residue.
I also on occasion rinse out my oil catcher pan with gas to keep the build up inside to a minimum and keep oily dirt from building up on the outside of it.