An additional point to consider is why is Cat6 cable considered desirable? Cat5e is rated for gigabit ethernet at the full 100 meters with no problem. Cat6 is not rated for 10 gigabit ethernet at 100 meters (may be OK at 55 meters). So there may not be very much upgrade potential in a Cat6 wired network. Cat6A cabling *is* rated for 10 gigabit ethernet at 100 meters, so that has much better upgrade potential.
Cat6 is rated for up to 10GB and double+ the bandwidth of CAt5e, which is good for GB. 6A is generally shielded, is good for 10GB across the full 100m, and has tighter specs on ACR, crosstalk, and AXT (alien cross-talk).
Hal is 99.99% correct. The only time you make a patch cable with any cat5/5e/6/6a is if you HAVE to have it now.
Is there really a difference? Online quotes show approx. 10 for $10 cat6 vs. 50 for $10 cat5.
Are these really constructed that differently? To the extent that putting a cat5 male end on a cat6 patch cable or 100 meter run will derate the transmission speed?
As mentioned, most cat5e is 24ga wire whereas cat6 is 23. The pins may not seat properly on the wire, or all the way down, so they dont lock in.
Other considerations: patch cords are made from stranded wire, and stranded wire 8p8c plugs differ from those made for solid wire; the pins/'teeth' on the insulation displacement are different (some plugs do fit both types of wire). Station wiring is always solid, so there's another problem with a field made cord. $10 for 10 plugs is a very high price; you should be able to find them for 1/2 that, even in a small lot like a 10 pack.
Field made cords are a colossal waste of time. A cheapie 1' cat6 cord runs less than a dollar from Monoprice, which is less than what the component parts cost (18" or so of cable, two 8p8c plugs, 2 strain reliefs), and it will be of the correct wire type and have molded strain reliefs.
A cat5e plug on cat6 wire might work fine for years, might prematurely fail, or might not go together at all...and that's assuming you have a good, proper crimp tool, know the wiring scheme (568A or B), and use proper techniques to make up the cord in the first place.