I have had stuff stolen from rooms twice over three years traveling in South America. Tips for better security:

• Don't leave valuables out in the room - some maids are light fingered
• Close windows, even if they have bars someone can put their arm through to grab stuff. I left a room for 10 minutes with window open. Bag under window was grabbed through window.
• Keep two wallets - main street one with just some cash and photocopy of passport. Second one with your credit cards and more cash that you hide in your room. I only take a credit or ATM card when I plan to use them. Getting a lost card replaced can take a week or more with DHL here.
• Keep your passport either in a money belt or hidden in your room. A stolen US or EU passport is worth about $2000 on the street...
• Follow your intuition - if a street feels bad don't go down it.
• Walking around drunk at 3am dramatically increases your risk of mugging. Pay for a taxi if you want to go out drinking. Leave valuables at home when you do.
• Don't display a lot of jewelry in poor areas
• Separate your cash stash into several hiding places in case you loose one, you will have the others.
• If you are renting long term get bars put on windows if you are on ground floor. Get a better door lock and metal lock protection installed (this prevent crowbar attacks).
• Change the locks. I have several friends who woke up to hear thief in next room who had got in with old key. If in backpacker room use a door stop. A chair under the door handle works too.
• Back up your camera memory card and laptop photos and documents  - at least if you loose them you won't loose your data too