1) Mess == Death to CPU/GPU/Motherboard/PSU/Etc. This is probably my biggest fear. I've sunk a lot of money into my system and I'd rather not see it go up in smoke due to a squirt of water.
My observation of reported failures is that nearly all can be accounted for in terms of "user error" in either the design, build, or operation phases. Design your system with sufficient 'idiot proofing' to prevent errors and catch them early. Build using solid conservative techniques, using good reliable components. Operate the system in a way that keeps it running (for instance don't forget to turn on the pump; designing so you can't forget to turn on the pump is part of idiot proofing)
2) Few good external interfaces. If I had room inside my case for a watercooling system, I wouldn't NEED a watercooling system. But taking it outside the case makes it nearly impossible to move. Are there any good ways of elegantly connecting tubes to or through a case?
You can get quick disconnects, the problem is that most add flow resistance, especially the ones that have check valves in both parts to reduce the need for system draining. However McMaster Carr does offer a few good ones. (I am NOT impressed with the Innovatek approach)
3) Draining the system. Are there ANY guides on this? How is it done carefully?
This is part of design in large part. Avoid loops that will trap fluid, Make sure there is a more or less straight up / down flow path so water can run out. Remember that to drain you need a discharge point at the lowest point in the system, and an air bleed point near the top. Also keep in mind that it is difficult to do a TOTAL drain, but it shouldnt be to hard to get most of the coolant out. However you are better off to minimimze your draining, since each time increases your chances for contamination.
4) Pump Death == CPU Death? If my fan dies, my CPU will get hot slowly and the motherboard should shut it down (in theory). With watercooling, it seems like the CPU will heat up VERY quickly and possibly die a gruesome death.
As mentioned earlier, not a big issue, or at least not worse than with fan cooling. Some folks have reported pump failures that led to enough convective circulation that the processor reached equilibrium at a much higher than normal, but still safe temp and was able to stay running.
5) Respected Resources. It's hard to seperate the serious people from the chuckleheads out there. What are good watercooling resources available out there?