I started to go down that road and gave up. I thought I was doing it to make the engine bay easier to work on, but it's more trouble to do hide stuff than to just deal with some clutter when something needs to be fixed. Even after tearing the entire engine down to the shortblock FOUR times and replacing the entire engine once, I still don't think it would have been worth hiding stuff. I'm not into showy engine bays for looks-sake. Nonetheless . . .
The first places to start are the vacuum lines and wire harnesses. Both of which would need to be completely re-routed and rebuilt from scratch to really hide them.
Make your own shortened plug wires
The smog equipment can all be pulled out if you can manage to turn off the EGR in the computer.
The A/C is up to you, but re-building lines won't help the clutter much.
Aftermarket intake tubes take up less room than stock
Fox TB conversion helps a bit
The battery can go to the trunk.
The CCRM can be relocated to the fender.
I wouldn't touch the ABS wiring unless you really know what you're doing.
You can custom fab and relocate the overflow bottle and hack the sensor.