Depends on how far you want to take it. The best solution is to build an equipment cabinet and mount the stuff in-wall with the wires hidden in the closet. But that's intense.
If you just want to clean stuff up, here is what I would suggest.
1. Figure out the shortest cables that will work. A 12' HDMI cable where a 1' one would do just makes clutter that really can't be cleaned. Monoprice is your friend here as they have cables in many lengths. Do this with all the cables.
During the original installation, I had originally taken the time to "dress" the cables on my system. It was uncluttered until I had to move some things around at which time I just let things fall into a rats nest. Damn.
If you think you're going to keep things more or less the way that they are from now on, it might be worth making it a project and tearing it down and building it back up in an organized way using velcro cable ties, etc. as jayn_j has suggested.
If you've got the system working well and after lots of configuration you can't remember which component goes to which input, etc. or maybe connections aren't your thing, you might want to do is to label each end of each cable before disconnecting. This will assist in getting things hooked back up as it's kind of difficult to trace identical cables once you start bundling them together in an effort to "dress" them and make them neater. You can use tape to label them and either write the name of the component and connection point or if you're confident in knowing what goes where, you may just want to put letters or numbers on each end (A----A, B----B, C----C, etc.).