fyi, if you're a trader (a facts & circumstances test) & you elect the mark-to-market method, the wash sale & the $3,000 capital loss limitation rules do not apply....
if the wash sale rules apply to you, there is a program by cfs inc that some of my fellow cpas use it for their clients...i only have a couple of clients who have wash sale issues & it's not cost effective for me to buy this program....try the demo & see whether it's worth it or not....