I believe it's been said before that the Cult of 1000 encounter cards aren't worth the hassle. The small benefit they could provide is heavily outweighed by the detrimental effects. However, as with all games I play, I tend to think of ways to improve under-used components (you should have seen some of my old Star Wars CCG decks, I was the only person I know who used Greedo regularly! *g*) and I've come up with a possible House Rule for the Cult of 1000 enocounter cards.
How about everytime you draw a Cult of 1000 encounter card you AUTOMATICALLY gain 2 Clue Tokens?