Use the right wallet for the right purpose.
First level are online wallets:
Online wallets are a good choice for everyday (small) payments.
Using bitcoind, paperwallets, or other more sophisticated setups for these day2day payments
will most likely compromise their security (carrying paper wallets with you, typing passwords
in public, using public networks etc).
Of course, online wallets should hold always only a very small amount of coins.
Second level are Internet connected clients:
Whichever you use (bitcoind, electrum, whichever), they are more secure as not on the Internet
in a central, easily attackable location. However, they are still connected to the Internet, and thus
might be compromised. At the moment, their security depends much on your knowledge of
computers and how you administer your local system. But: no matter how good you are, there's
a risk. These wallets should therefore never store more than a moderate amount of coins.
Third level is cold storage:
No matter what you use (paperwallet, electronic), these are private keys that never touch any
machine that is connected to the Internet. Most secure, and also least practicable. Creating a full
setup with a locked-in computer for efficiently signing lots of transaction offline is work, so it's
not always feasible - especially for the average user. This is where paper wallets come into play:
secure, but very little organizational overhead.
In the end, the most important thing is to use all three levels for the right applications and
the right amount of coins. If you go exclusively cold-storage, you will most likely compromise
your security sooner or later due to the impracticality of this solution (ie, whipping out your
unconnected laptop to pay for a restaurant bill). Exclusive online wallet usage is bad for the
obvious reasons.
The amount of coins in each of these levels can only be decided by yourself.
Online wallets: what you can afford to lose without causing a major problem in your life
Connected clients: what you can afford to lose without destroying you
Cold storage: the rest