I have used a self designed database logbook for since 1986. Unfortunately it was done in DOS. Printing became a problem in XP and program won't even run in Vista. So a couple of years ago I searched for a Windows based logbook that would let me import all of my DOS info, over 20 years worth. Logbook Pro was the best program I could find. It is easy to customize to let the pilot track anything they want such as mountain time or long line time. I recommend it. Keeping military time seperate from civilian time would be a piece of cake.
Logbook Pro and APDL Electronic Flight Log Software