Best practice for long-term storage of Bitcoins is storing the private keys to your wallet on acid-free paper. Point blank. Digital files can and will be corrupted, no matter what format you use. They *probably* wouldn't become corrupted after only 3-5 years, but I certainly wouldn't risk a large sum of money on it. Paper files in a fire-proof safe are the only safe long-term option.
You can dump private keys from your wallet using any of the common clients: bitcoin-qt, Electrum, Armory, blockchain.info, etc. Just make sure you delete the wallets from your non-backup locations so they don't accidentally given away with an old computer.
If you're worried about your safe getting compromised, you can encrypt the bare keys before you print them out using gpg or something similar. Just make sure you can remember the key! Store it in another location away from the safe since you'll likely forget it after 5 years.