Balanced or unbalanced?
Patchbays increase the amount of cable in your system, and this makes hum and noise rejection even more important. A balanced patchbay works for unbalanced applications, but an unbalanced patchbay can never be a balanced patchbay. With inexpensive options like the Re'an and Neutrik supporting balanced connections, there really is no reason to go unbalanced. Make an effort to purchased TRS (tip ring sleeve) cables and snakes and you'll build a foundation for a flexible, balanced system. Hosa snakes are inexpensive and work fine as long as you provide strain relief when wiring your rack. Hosa also makes short 1/4" TRS cables in 'patch bay packs' for front panel patching. Of course, these are perfect for short cable runs behind your rack, like those from your mixer to the patchbay.

Using a spreadsheet to plan a patchbay - Stage One
In one column, list all the inputs in your system. List everything, even though you might not use it. Some creative options may occur to you when filling in gaps in your patchbay - like mating the aux outputs of your mixer to the external inputs of your synth. Be sure to include every mixer return, audio interface input, effects input, and sidechain. Do the same for every available output.

Here is an example excel file for planning a patchbay. It should work under both Mac and Windows - but I have not personally attempted to open it on a windows machine.

Stage Two
Begin mating logical inputs to outputs for normalization. Normalization allows an input to be routed to an output without a cable plugged into the front of the patchbay. It behaves as if you plugged a cable directly from input to output. In your spreadsheet, move outputs to inputs like you would if you did not have a patch bay. For example, Kurzweil K2500 outputs 1 & 2 are sent to mixer inputs 1 & 2, Lexicon outputs are sent to return 1 & 2, Mixer stereo send bus to Lexicon inputs, etc...

Keep an eye on stereo/mono issues with your mixer. Many line mixers have a bunch of stereo inputs that also serve as mono inputs if only one cable is plugged in. It helps to allocate stereo and mono inputs in a way that makes sense for the way you work. Some sends and returns may be mono or stereo, be sure to plan accordingly.

As you work your way down the list, the signal priority should reveal itself. When you run out logical normalized connections, which usually happens shortly after you finish mixer I/O, begin a list of non-normalized connections for straight ahead patch points. Outboard processors such as compressors and EQs are good examples of this.

Stage Three
Now you take your I/O pairs and try to fit them into the available patchbays. If you have a 48-point patchbay (24x2) then take the first 24 inputs into your mixer, with corresponding outputs, and slap them into rows 1-24 of your spreadsheet. There. The first patchbay is done. Continue until you run out of patchbays. If you have extra patch points(!), create some mults out of two modules by wiring the output to the input. However, chances are you need to make some difficult decisions about squeezing all your I/O into the available patchbays. Again, the spreadsheet makes this process easy.

At this point, your spreadsheet is complete and can serve as the master plan for your patchbays. Wire at will.

Labeling
I use Freehand to create patchbay labels. Text objects can be created and distributed automatically. Here is an example file for a Re'an patch bay designed for 8.5x11 paper. This is smaller than the width of a patchbay, so you'll have to tape the two sides together to form a single strip. The result can be affixed to the patchbay with a small piece of tape.

Color coding can really help matters. Highlighters can be used to unite logical groups that got separated in the quest of normalization pairs. Sends and returns have a habit of throwing the input and output of a signal processor in wildly different placces on your patchbay. Highlight them. Mults can be grouped by color.