While playing house poker, does a natural 4 of a kind beat a 4 of a kind with wilds?

Key word is "house poker", if you are playing house rules, then maybe natural beats wild. But it shouldn't. 4 Kings beats 4 sixes. Natural shouldn't matter... but again, it's up to the house, I would just hope the house explains the "house rules" when they are different than normal rules.

As LegFuJohnson suggested, unless you actually made up a specific rule which stated natural 4-of-a-kind beats ANY wild card 4-of-a-kind, then you'd always go by the rank. Personally I think a made up rule like that would be ludicrous, but if it's your own house game, you can make up anything you want. You could even say that "around the corner" straights are allowed. (Queen, King, Ace, 2, 3 and junk like that.) That would be equally ludicrous, but it's your game.

you best of making the rules before you play, but 6666 is much much harder to make than 666+joker.

natural wins

Four Kings is better than four Sixes. The four Kings win. There should be NO questions about it. If a natural hand beat a wild hand, there would be no point in playing with wilds. Otherwise, 6,6,6 (natural three of a kind) would beat 2,2,3,3,wild (full house with a wild card).

In your situation nautral wins, if you are looking for some poker calculator check this out http://www.firstpokertips.co.uk/automatic-poker-calculators.php

As others mention, anything's possible in house rules but normally the rank would control irregardless of natural vs wild. Somewhat more likely might be in the case of ties...then you might see KKKW9 beat out KWWW9 - again, all depends on what the local house rule is.