I really liked this short post by director/designer Nathan Ford on the advantages of custom cut web grid systems. Here’s the money quote:
Nathan Smith built 960.gs a few years back and it went a long way to popularize the application of grid-based layout on the web. This was a leap forward in bringing grid-based thinking to the web, but 12 columns at 960px wide has become so ubiquitous now that it limits our progress into more considered and complex grid design. 960.gs – and most frameworks – invert a key aspect of grid theory:
You should design a grid based on your content’s constraints, not design your content based on a grid’s constraints.