It all depends on the value of your Bitcoin and what you use is for. Are you saving Bitcoin for hopes of future increase in value, do you trade it frequently or do you use Bitcoin to purchase goods and services. With that said the safest method is a paper wallet. But a paper wallet makes it difficult to buy,sell and use Bitcoin frequently. I have found that the solution that works best for me is a combination of storage alternatives. A paper wallet for saving your bitcoin (think of it like money in a bank vault), a coinbase account for buying and selling frequently (like a brokerage account) and a iPhone app for small purchases (like pocket money).
Definitely the best way to secure your Bitcoins is Bitcoin Hardware wallet like Trezor. It allows you to securely cold store your Bitcoins and also allows easy spending when you need so.