Has there been an explanation as to why they were using DES? Gawker started in 2003, a year after DES was superseded by AES, and there were plenty of more secure algorithms being used at the time.
If you have to develop a secure solution you make some research and choose what you think is a good solution (and if it is something outside your field you study/ask).
In 2001 I've to implement a secure solution for a mobile platform, I choose Rijndael (them picked by NIST for AES). My previous knowledge of encryption algorithm was near zero.
And then if you make the wrong decision, on something important as security for a public website, over the years you iterate (come on, till 2003 nobody internally thought it was a must to fix this mess?).
If everyone did this we wouldn't have these discussions so often. The problem is that people think they know about crypto, and think they know what they're doing, and probably won't believe otherwise until they get smashed wide open like this. This applies to almost all areas of knowledge, it's just particularly damaging in crypto as it's arcane and very sensitive to changes, often in very subtle ways.
So when it comes to implementing a password storage system I read up a bit, get confused, ask a couple of people and get different answers back.
It's the "get confused" bit that's dangerous. As you say, the differences are quite subtle and (for me at least) when they are being explained make perfect sense, but ten minutes later have become an uncrackable cipher all of their own.
At the moment I use Authlogic in Rails, which uses SHA512 by default (SHA512 is built into the Ruby core libs).
But I also notice that it's quite easy to switch to bcrypt (using the bcrypt gem).
Is it worth switching? Or at least using that as my default on new apps?
Bcrypt is slower than SHA512, in fact it can be made to be very slow. This is actually ideal for password hashes, it doesn't matter if it takes your server 50 milliseconds to calculate a password hash but that would severely slow down an attack.
It is important however that they are being used correctly. Either would be a good solution if properly salted.
At the time they implemented this (~5 years ago) most PHP tutorials just pointed to either crypt or md5. The other cyphers and functions were either added later, were not in stable PHP branches at the time, and/or most common tutorials had not picked up on them.
It is also a pain to port your password storage method