Ahhh... seems to be a problem that we have all had for a while now. There are several ways to tackle this problem, but here are the basics.
First, how much to you tinker with your box? If you do alot of work to it, you need to keep your cables as free as possable. Using that pastic tubing that you get from radio shack (-cant remember the name for that stuff!!-- AHH!) to organize your cables would be a good start. Personally, i can't stand the stuff, but it will cover the wire bundles good enough. Also, it will offer the flexability you need to move cables around.
Now, there is a style that takes a while to perfect, but it involves lots of zip-ties. You can really control the way your wires run, but it is easy as heck to make it look like *hit as well. That is something that you will need to practice alot of. But if you decide to start using lots of those things, you have to realize that this is more of a permanent way to go. Once you have a bundle zip-tied, there is no easy way to fix it. Not to mention that if this is done -correctly- it can look awesome.
Now layout is the most important part. You can use your ribbon cables to hide alot of the power wires, but you have to take into consideration what parts of your computer you will be working on the most. Now anybody that has been around computers for a while knows that the higest traffic areas around computer cables are the easiest to tangle. The same with the inside of your computer. Organize and plan ahead.
For airflow, I think the best way to fix that would be good 'ol electrical tape. Use your imagination. To heck with the looks. ... eh?