In reply to Pietrach:
Whilst I'm sure that someone wil come along shortly and tell you that man-eating salt-water crocodiles can live in second-hand boots and that unless you treat them with a particular product you'll be eaten alive feet first, I'd just give them a wash.
A proper wash, mind. Lukewarm water, laces off, footbeds out, using Nikwax footwear cleaning gel or an equivalent to remove any mud, dirt or stains from the outside and using your fingers to rub it in properly as the applicator pad on the outside of the bottle falls off quite quickly. Fill gthe inside of the boot with water and empty it a few times, putting your hand inside and rooting out any compacted fluff or dirt. Remember to wash the footbeds too. Then give them a thorough rinse under a running tap so that the cleaning agent and any dirt or other stuff that you've loosened is washed away.
Then you have two options depending on which waterproofing agent you're using.
If the waterproofing stuff has to be applied to a dry boot, then put your clean boots on an old towel or rag in the sunshine to dry; a sunny window sill is ideal but anything more direct, like in front of a fire or on a newspaper isn't good. Fill them loosely with newspaper while they dry, remembering to change this a couple of times; or just leave them open as you wish. Change their position a few times so every bit gets some sun. When they're properly dry - as in, a day in the sunshine dry - put your waterproofer on, then when that's properly applied and soaked in, put the footbeds back in, lace up sand you're good to go.
If the waterproofer has to be applied to a wet boot, get this on before you go through the drying process. I've found it best when the boots are damp rather than sodden. Then get the boots dry as above.
And that should be more than enough to get your boots clean and ready for your feet.
T.