In the Navy, huh? Thanks for all you do!
I use both AMD and Intel processors in my builds depending on client preference. I actually prefer AMD as you tend to get more bang for the buck...their Phenom quad cores are hard to beat. That said, AMD chips tend to run a little warmer than the Intel chips of comparable performance, so cooling is a consideration. A case with good airflow is essential for high performance machines regardless of whether it's AMD or Intel based.
The FSB and cache size question is really pretty dependent on which processor you go with. The Phenoms I like best (9950 Agena) don't have an overly large cache, but they perform very well with higher FSB capabilities. With some of the Intel chips with larger caches, the FSB is not as big a concern.
I use ASUS motherboards almost exclusively. In the years I've used them, I've only had a couple of boards go bad and have never had a DOA. ASUS has always replaced the boards, no questions asked. Many times an apparent board failure can be traced to the end user not setting the board up properly for their system.
I'll leave the LAN question for the gamers here to comment on.
The difference in 2000MHz and 1600MHz RAM is barely perceptible (if at all) to the person using the machine, but the 2000MHz module will require more power than the 1600MHz module which means more heat to dissipate. The trick here is to choose quality RAM that's properly matched to the motherboard. Don't skimp on RAM.
Water cooling has come a long ways in the last few years and several manufacturers offer good liquid cooling solutions. Some motherboard manufacturers build liquid cooling capabilities into their boards...I know ASUS offers a couple. I've used only the Corsair Nautilus, and found it to be easy to install and very effective, but I'm with Neil....I prefer air cooling. With the right case, air cooling is pretty darn effective.
I'm sure some of our "build freaks" will offer their opinions here, as well.