A few people pointed out MyMonero.com as a good web wallet. In your opinion, can the site be trusted to hold my Monero funds securely for a while? And is that the user fluffypony's project?
You should never trust any web wallet regardless of who is developing it. Just like you should never trust any exchanges with your funds. The largest theft of coins originated from compromised online web wallets (blockchain.info), exchanges (Gox/Mintpal) and marketplaces (countless). Trust yourself and your own system and never take advice from anywhere who says otherwise.
The biggest problem with XMR paper wallets right now is the lack of an easy way to use the view key to verify a balance.
For example if someone sends XMR to your cold wallet how can you verify that transfer? You cant unless you run the daemon and turn the "cold wallet" into a hot wallet.
Finding a way to make the view key function work for users should be a top priority. Until then cold wallets are only good if YOU are the one who send the XMR to the cold wallet (from a hot wallet under your control).
If I am wrong and there is a way to use the view key to verify payments send to a cold storage address please correct me.