I use GSAK to keep track of caches on my PC and Cachemate on a Palm III when I go hunting. I have not come up with a good way of keeping track of the coordinates for "puzzle" caches though. I have a number of caches that I have solved and am looking for a good way to keep track of them along with the data downloaded from geocaching.com. The little slips of paper are constantly getting lost.
If you are one of the cachers that use the same equpiment, how do you handle the additional coordinates?