For starters, all documents should be kept in a waterproof document holder (Heavy duty Ziploc bags are a cheap alternative).
It is best to keep all your original documents on you at all times, do not trust them to the hotel or hostel safe, especially in third-world countries. Furthermore, never keep your documents in the same pocket as your money. In the unfortunate event of a mugging you can hand over your cash without endangering your far more precious documents. Keep photocopies of your documents in the hotel/hostel safe or in your main backpack, this is your backup in case you lose of all your originals. Do not keep your originals and photocopies in the same place!
Make sure you know the entry requirement for your destination in case they require special documents.
A good tip is to print out this page and use it as a check-list while packing.