Use "mouse bites" which are little bridges with holes to make them "breakable" like this:
The grid in this graphic 0.025 inches so you can work out the dimensional details. There's no standard tool for creating these bridges. You just have to create one and then copy and paste and then bridge all of the gaps. It's all dimension layer.
Then use DirtyPCBs and submit it as one board. The result is like this:
Developing PCBs for the most using constructions: is it interesting?
Other board houses might support mouse bites too but I've done this twice with DirtyPCBs and I have been very satisfied.
As for ribbon cables you can save a LOT of space using FPC cables:
Molex FPC 1mm
like Molex 15167-0243 but there are many varieties of contacts, contact orientation and length of course.
For connectors I use Molex 52271-0879 but I'm moving to 52030-0829 because they can be inserted in 4 different orientations which minimizes conflicts (especially if the pin assignments are symmetric).
Here's an example:
This might look a little nuts but it works fine. I run all digital, leds, relays along the bottom of the unit using FPC cables like this. In this pic I didn't bend them nicely but you can fold these cables completely over on themselves (they're actually quite tough) so that they can run at just about any angle and still be flat. With some practice it can be much neater.
I don't use ribbons for audio though. For audio I use conventional hook-up wire or shielded cables where appropriate.
For board-to-board you might consider conventional breakable headers like this:
In this particular example I used Molex 929834-07-36 headers which are much longer than the conventional breakable headers. They come in other lengths of course but this one is 1.25 inches overall so it can span 3 boards. With female receptacles on the ends the boards can be separated. Probably need to mockup with Sketchup to get it right though.