If I have all the hardware as I want it, I will usually take a little time to route the cables. I have quite a few older desktops, so I'm constantly switching out different pieces of hardware. Its very annoying to zip-tie something, and then have to cut it an hour later because I decide to add another HD.
This also brings me to the point of modifying cases. On one of my half size cases I twist tied a GPU fan to some HD power cables. This appears to cool the HDs, even though if the case was moving, the fan would probably fall off. I have also managed to put 11 HDs into a case designed for 2. This required IDE and SATA cables to be stretched a little farther than usual so I had some problems making it look neat. The biggest problem I had was keeping the fans in places away from cables.
I guess if I had to summarize, I would say that I keep the cables out of the way, but don't make sure they are perfect in each hole in the case. It's just too much trouble to re-run the cables all the time. Maybe I'll spend more time when I get a glass sided case.