We're doing a monthly handicap tourney with 3 qualifiers and the final round. All are on the same course, but with different conditions. The 3 qualifiers are unlimited play and the average scores represent one's handicap. The final round is single play.
Scoring works like this. The average for your 3 qualifiers represents a par for you. The winner in the end is the person, who gets the closest to his qualifying average (or better, of course) in final single play. For example, if my Q avg is 60 and I score 61 in the final, I'm +1. If a hack averages 82 in qualifiers and scores 81 in the final, he's -1 and he beat me by 2 strokes, etc.
This system has been working great for us for the last 6 months, but you can only do it in a CC, where you actually know just about everyone and you trust them completely to actually do their best in qualifiers.
P.S.: Another way to go (but it requires more effort) is to create attractive enough tourneys for most to enter (4 or 5 should be enough) don't tell anyone they're for handicapping purposes and calculate handicaps from those scores.