Keeping a long term base in DayZ
As many players specifically watch for bases/hidden caches etc, the only real technique to protect your stash is to work in a small group of individuals to have continuous activity on the server.
Of course, you'd need to trust your little clan...which is perhaps a separate issue :-)
Two Answers:
Some people consider this hacking, and I personally don't do it, but putting a vehicle in a somehow bugged spot (so it's stuck in a wall) makes it impossible for helicopter teams or snipers to find it.
If it's against your ethics of the game, or you simply can't find a buggy area, the best solution is not to have a permanent base. Go sort of "nomad" style, and hide it in a forest every time you log off. Simply go where the loot is, and move it at least once a day. If you won't be able to log on for a while, put it in the southeast. loot hunters never seem to look there.