Several other posters have covered the standard ideas already, but I'm seriously OCD about cable organization, so I'll hit a few points again.
Plan your wires first. For example, my PSU has a couple of lines with only a single molex plug, a couple with only fan plugs, and a few standard 2 molex and 1 floppy plug. If you only need 1, run one that only has 1. It sounds obvious enough, but I know when I first put a machine together I really don't give too much thought to it.
Secondly, consider reversing your hard drives. You can tuck the cables back and around the drive cage and keep them out of the way. This also keeps all of that extra cable from hanging around, incase you don't have cables that are only 3-4in.
A good key rule is that nothing crosses the motherboard. Pick up a bunch of tie mounts and zipties and use them to run wires around the edge of the case. For example, my 12V is to the left of the CPU under the PSU, but the cable is really long--so I use tie mounts along the top and inside of the back of my case to run the excess cable around. You can completely "hide" the power connectors for your rear fans and GPU fans that way too. If you've got enough slack to keep the actual molex connectors on the top of the case, it'll look really clean.
I wouldn't worry about a modular PSU. It's a great idea, but making your own modular seems excessive, and if the one you've got works, why replace it? Run *all* of the wires you can behind the motherboard, and tape the ones you won't be using out of the way on the back.
I recommend running *all* cables through back there unless they connect on the left side of the motherboard--especially drive cables. You can bring them back out right by the drive cages, ATX connector, et cetera and hide the slack around the back of the motherboard tray.
Also, even though you already seem to understand this part just fine, zip tie the living hell out of things that are close to each other. After you finish this, you really shouldn't have many power cables or anything similar to zip tie together, but your motherboard connectors, additional USB plugs in the back, et cetera all have a bunch of wires that you'll never be able to really do much with--so just zip tie them together and tie mount them as out of the way as you can. Some people cut a piece of plexi to place over all of these wires at the bottom, but even I'm not that anal.
Good luck!