The process of actually cleaning up the cables within a system is going to vary from build to build, obviously. The best advice we can give is to give each cable some attention and route each one as neatly as possible.
It's best to snake the cables behind the motherboard tray and to not tie anything down until every cable has been connected and is roughly in the ideal position. I like to route and connect any front-panel or case-related cables first. Then I install any data cables for various drives, and finally place in the power supply. If you throw everything into the system willy-nilly and connect it all up, you'll often find yourself disconnecting or moving things around to get the cabling right.
Keep airflow in mind; don't cover any case fans or coolers with a cable if at all possible.
The vast majority of the cabling should wind up behind the motherboard tray in many builds. If your case doesn't have cut-outs in the motherboard tray, try running all your cables along the side edge of the tray to achieve a clean look.
Once you've placed all of the cables, start securing them in tight bundles, starting from the top of the case and working your way down. If any cables are especially long or have excess connections, consider tying the cable together to prevent it from getting in the way of other components and cords. In most cases, you'll find a large space — relatively speaking — toward the bottom of a system where the bulk of the excess cables can be hidden and secured, as well as ample room behind the motherboard tray.
Velcro strips and twist ties are ideally suited to PC cable management, and adhesive tie downs can also come in handy if your case doesn't already have tie down locations built-in. Heck, you can even use rubber bands! Don't use zip ties if you can avoid it, however — if you ever need to remove a component or rewire your PC, zip ties have to be cut away, and it's all too easy to slice a cable in the process. Stick to reusable, removable ties if at all possible.
Now that you understand the building blocks of smart cable management, you may want to see smart cabling in action. Check out PCWorld's guide to organizing your PC cables for a complete system build that discusses proper cable management each step of the way.
What about the outside?
If you're looking to tidy up the cables on the outside of your PC as well, all of the same suggestions apply. Disconnect all of the cables and reconnect them thinnest to fattest, giving each cable some individual attention. Connect any thin audio cables first, then move on to the USB cables, Ethernet cables, and power cables. Route each cable neatly, making sure not to create any tangles along the way, and then use Velcro strips to create tight bundles. Spiral wire wraps can also be great for tidying up the cables outside your PC.
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