I just found this thread and read a bunch of it during lunch. Lots of good info! I'll add a few bad decisions I've learned through my own experience, or that of my friends...
(Edited to shorten it... I got carried away.)
Electric Fans. They Suck. Period. It takes just as much HP to turn that alternator to drive your electric fan as it does to turn the mechanical fan. Nothing is free, people. And whenever the fan isn't running, and you're not moving much, the underhood temps go sky-high, which causes all sorts of things to eat it. (Alternators, computers, vapor lock, brake booster even...)
Snorkel. If you're in water over the hood, you should either do a better job of checking water depth, or SLOW DOWN. My TJ has been in water just over the top of the front fenders (~36") without issue, and about the top of my 33's lots of times. Never even been able to find water in the factory airbox... YMMV depending on vehicle of course.
Lifts bigger than about 2". Shaky business, but I have yet to meet a lift kit over about 2" that was worth the tradeoffs. My TJ is 1.5" to 2" over stock, via a combination of OEM (not OME) Jeep springs and factory isolators, and I'm running stock length shocks with a few spacers there as well to get proper droop travel. It flexes like a slinky, rides and drives like it's stock, and there's no squeaking bushings, welded arms, cheap bolts, or powdercoating anywhere, and the front/rear spring rates are spot on. It just works, because that's how it was designed, by people with actual engineering degrees who could take into account things like overstreer/understeer, ride rate and frequency splits, and overall long term durability.
Heavy stuff. Anything that adds weight to a vehicle that you're trying to take offroad must be considered carefully. Adding significant amounts of weight puts undue stress on components, and causes lots of things to start going wrong. This is one of the main reasons that older Toyotas were so "strong". They were light enough that it was hard to break them with their own weight.
Dual Batteries. Ok, there is a place for them... If you run battery intense loads while camping, they're a great idea so you can burn one down, and still start the truck. Or if you're plowing snow with a 63 amp alternator... But if you have a modern vehicle with a 100A or likely higher alternator, one battery is plenty. I can melt the wiring to the motor on my winch before drawing my normal Group27 battery down. While the winch cools, the battery charges. You're just adding weight and maintenance issues with dual batteries.
Winches that don't have a "W" on the front. Been there. Done that. If it doesn't say Warn, it has let me or someone I know down.
Beadlocks. I don't know what people are doing that necessitates beadlocks on anything short of a desert racer or all out rock buggy, but I commonly run 10-15 psi on the trails, and I have NEVER had a bead come off. I run 4.5psi in the sand, and haven't lost a bead there either.
Ok, enough from me. Of course all this is from my experience, so if you've got an exception, that's fine. But I knows what I knows, and just though I'd share too.
Chris