I've got one of those Kryptonite D-Locks, while it is great, it's heavy.
If you are using it for commuting, then it's fine if you can leave it locked up on a rack at work so you don't have to carry it around. That way you can then get a decent rope/chain lock which isn't quite so heavy, but you can carry it in a bag and will be much more useful if you need to stop somewhere and need to quickly pop in a shop.
As ideally, the best form of protection is two locks like described above.
As for securing parts of the bike, I'd say it comes down to how secure you think where you are leaving it is going to be. Of course leave it on a city street with unsecured expensive wheels or saddles and chances are it will get pinched. But even in a secure place, it only takes one unscrupulous co-worker or neighbour to take something.
In my personal experience, the block of flats I live in has a bike room. I secured my bike with two locks and pinheads for the wheels. One day I found that one of my neighbours had decided to nick my bottle cages. So that then made me realise you just can't trust people and now I keep it inside my flat. You've also got the fact that with bikes closely locked up together, there are many people who use bikes for commuting who just don't care for their bikes and they are total wrecks, so won't care if they slam theirs into yours.
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