We've all seen the full range of Jeeps, from bone-stock mallcrawlers to huge monster trucks. Somewhere between those two extremes lies the perfect size. "Perfect" has a different definition for every Jeep owner because it depends upon what type of terrain they intend to drive on and how they weight the ration between form and function, but building it "perfect" for your needs keeps the cost down while maximizing its capability where you need it to perform.
Before selecting your Jeep's suspension, you must first determine what size tires you want to run. Suspension height must match the tire size or else you're compromising your Jeep's performance.
I happen to value function over form. I don't care for glitz and glam; I laugh at huge lift kits, tremendously oversize tires, and blingin' wheels. I mentioned before my intended uses for my Jeep, and since then I've spent quite a lot of time researching and weighing the benefits and compromises between my various options. I am approaching my Jeep's buildup from an engineering standpoint because I'm not trying to impress anyone but myself.
Primarily, I want a proper suspension-height-to-tire-size ratio. Too tall a lift requires expensive driveshafts, poor steering geometry, compromised ride and handling, and a high center of gravity. Too low a lift results in tire rub, minimal suspension up-travel, and a belly & rocker panels that take a beating off-road (especially with the Wrangler Unlimited's shallow breakover angle that comes as a result of the long 116-inch wheelbase). Big tires look great and can perform very well in certain types of terrain, but they come at the expense of driveability, cost, wear-and-tear, and comfort - not to mention prowess in other types of terrain. Small tires limit traction and clearance under the axles for trail obstacles.
We've all seen Jeeps with far too much suspension lift for the size of tires they're running. A high center of gravity (C.O.G.) leads to instability in off-camber situations, a greater propensity to roll over during emergency-avoidance maneuvers, and wasted money since a taller suspension requires more parts than the minimum lift needed to fit that size tire:
The opposing end of the spectrum is a "Low COG" build like the Lower Forty that Mopar built from a JK with no suspension lift but extensive bodywork to fit 40-inch tires. It looks good and is very stable for the given height of the tires, but it can be even more expensive to make the sort of fender modifications to fit those tires than simply modifying the suspension:
The other issues to consider are the significant effects that tire size has on gearing, clearance, driveability. As tire size goes up linearly, their street driveability declines exponentially. Teraflex put together an entertaining little video discussing these issues regarding tire sizes on the JK: