If you use it correctly, ISO 9000 can be a positive thing for your software company. Here's the secret: Observe the procedure, don't dictate it.
There are two ways of looking at software development. Some people like to look at developers as artisans. They spend a lot of time on a single application, but when it's finished, it's like a really high-quality chair - it's really pretty to look at and works really well. Other people look at developers as assembly-line workers. They kick out a piece of software according to spec, and pass it on down the line to the next worker to glue in. This software is like a chair you can get at Wal-Mart - cheap and quick and does the job.
The truth, as is so often the case, lies in between, but there are a couple of undeniable facts: Not every software developer is an artisan that can make a really great chair. And even if they were, once the original developer moves on to something else, who knows what uses his chair will be put to? So whether or not software is craftmanship or assembly work, procedures are probably going to be necessary for making changes. And in the software world, if you're not making changes, you're dead.
The true raison d'etre for ISO 9000 is that processes can be improved. But you can't improve your process until you know what it is. So observe. Find out what your developers are doing, how they spend their time. (Ask them how it could be better, too. You won't always get a useful answer, but software developers are usually pretty darned opinionated and will have something to say.)
Now you know what your process is, you can document it, and you're most of the way there to your certification. And you'll be even further along once you document how you're going to accept suggestions for improving the process.
Once all that is done, you can change the process. You might see a lot of improvements in front of your nose, right after you write everything down. If your developers tell you they have to get 17 signatures in triplicate before they can issue a fix, you've got room for improvement.
But it all comes down to knowing the procedures. The easiest way to know them is to write them down. And once you have them written down, you're most of the way to your ISO 9000 certification.