Just skimmed through this and looks a very comprehensive guide with much good advice, however I have to take issue with this :
Before you even begin to lay out your PCB, you MUST have a complete and accurate schematic diagram.
Many people jump straight into the PCB design with nothing more than the circuit in their head, or the schematic
drawn on loose post-it notes with no pin numbers and no order. This just isn’t good enough, if you don’t have an
accurate schematic then your PCB will most likely end up a mess, and take you twice as long as it should.
at least the 'complete' part. These days most designs will have at least one microcontroller, on which many of the pins can be exchanged to improve PCB layout. Ditto FPGAs, and often connectors to other parts of the system, as well as series combinations of parts that can be swapped.
If the design is of a complexity level that you
can hold it in your head or a few scraps of paper, then diving straight into the PCB placement and layout is likely to produce the best layout from the point of view of minimum trace lengths, minimum vias, better EMC, better manufacturability, and maybe even fewer layers.
The best allocation of pins can only be done whilst placing and routing the PCB, and back-annotating all this to a ready-drawn schematic is a recipie for errors to creep in. Unfortunately I've yet to see a schematic package that deals well with a vague "This bunch of lines goes to some of these pins, in an order to be decided later" sort of specification. There are so many things that can potentially be swapped around that trying to specify it in a schematic would take way longer than just placing & routing it and documenting it in a schematic afterwards.
Obviously this approach doesn't scale well to more complex systems, and is only applicable where the same person is designing the circuit, doing the PCB and probably writing the firmware as well, however even then, keeping maximum flexibility in allocating pinouts can make the PCB layout process quicker and finished result better.
Most PCBs have mechanical costraints, and simply looking at where parts _can_ go on a layout is far more productive than trying to "draw the schematic with the PCB in mind".
On a similar theme, I recently found this
very comprehensive guide to PCB manufacturing issues (PDF) - although specific to one supplier, the general rules apply to any PCB that is going to be manufactured