We had a 16 team league and I used Perfect Secretary for the scores/standings, and an Excel spreadsheet for the money. It's been a while since I was secretary, and there may have been upgrades to allow you to track the money too.
I addition to the standings, averages, high game/series, etc., it also would print the application for honor scores shot during the week, including over average (game/series) and awards other than the standard 300, 299, 298, 800. I never used it, but I think it also allows you to post your standings on-line. The cost of the program was taken out of the prize money upfront, and in my opinion, is worth the investment.