Try
www.logbookpro.com. I have been using it for three or four years, and it's superb. Although it's a bit American in places, the user can customise almost everything so it would be ideal for the military.
I use it for both the C208 and my day job on the 737 and it's sufficiently flexible to do most things. The printed reports can be in standard Jeppessen format, or customised spreadsheet (to replicate the RAF logbook if you wish), and the CAA accept it on disc.
Cheers.
MoT