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Here's are really simple tip: If you don't already, store your funnels in a plastic bag, drawer, box, etc., so they are always clean when you need them. I thought most people did this until I helped a friend change his water pump and radiator, talk about lessons learned the hard way!
I keep my funnel on the floor leaning up against the wall. I have the small end sticking in a plethera of paper towels with a Home Depot bag stratched over the big end to keep dust and spiders out of it.
I have my "long" funnel hanging up under a shelf in my garage. It has a tab with a hole in it that a finishing nail will go thru. I made a cover for the big opening by slicing a slit to pass the tab in a plastic food bowl of the appropriate size. I stuff a twisted up scrap of paper towel in the small end to hold drips and seal the opening. I keep my assortment of other smaller funnels in a plastic bucket with a lid. I also have one of those $5 funnels from the parts store with a built in cover, measuring lines, twist open valve, filter screen, and a plug in the end of the hose.
I store mine on a shelf under my workbench with rags stuffed in it to catch the drips and to keep most of the crud out. I also wipe them out before and after every use.
you can buy great funnels which have a lid that screws on the top and one that screws over the bottom end. sounds like a pain to use, but its not and there is no way to keep a funnel cleaner.