CLS/E-TTL vs Pocket Wizard (and others)

When picking a method to trigger your lights, it boils down to Radio or Infrared.

Canon E-TTL and Nikon CLS use infrared technology to transmit their camera information between flashes and body. This information contains values for light output, distance between subject and camera, and exposure settings - shutter, ISO, etc. Infrared can travel only a short distance of about 30 feet so range is limited. There are ways to extend this range by bridging flashes or by use of Radio Popper's line of products. Also, there is a line of sight associated with infrared technology, typically 30 degrees from the master flash/ camera body. When placing your flashes onto your environment, the unit's IR port must be openly visible to the master controller, otherwise the digital data for exposure cannot communicate.
This technology comes real handy to wedding photographers or photographers who need to act quickly during the shoots. E-TTL and CLS take loads off the photographer when it comes to calculating exposure; they won't have to tweak the settings to get a proper exposed shot - as defined by the camera. There is no need to physically get to each flash unit to adjust the settings because the settings can be controlled from the master flash, usually on your camera.
No other adapters or special add ons are needed to work. You only need are a flash that can act as the master unit such as the 580 EXII or SB800, and all the other flashes could be master units or slave-only units. Take note that not all Canon and Nikon flashes have the built in wireless feature. The oldies won't have this technology.

Radio sends signals from all around. They can pass through objects and walls although the range will weaken. Companies that produce these radio triggers (in order of pricetag) are: Pocket Wizard, AlienBees CyberSync, and soon to be Radio Popper with their Jr. line. Radios have proven to have longer ranges, PWs having to have a range of 1600ft.

So far, these manufacturers have made their triggers to transmit only the 'fire flash' signal meaning that no automatic exposure information is sent through the radio. Photographers are forced to use manual mode on their flashes; we have to adjust power level, zoom, distance from flash to subject and groups/channels by hand by walking up to each unit and dialing in, or pressing buttons to change the settings. In contrast to the built in, self functioning units mentioned above, Radios will need an adapter to trigger the flash whether it be PC male to miniphone male, hotshoe to miniphone, etc. At least in this fashion, radios are compatible with all flashes ever made to date.

In terms of price, either method will be the same with an exception.

1)
You choose E-TTL/CLS and the flashes you need will be in the upper tier.
Price depends on amount of flash units.
expensive flash + expensive flash(es) = your max budget

2)
You choose Radio and the flashes you need can be in any tier, cheap low end through latest and greatest.
Price depends on amount of flash units AND radio units. (assuming you pick the low end, cheap flashes usually around ~$100)
inexpensive flash(es) + expensive radio(s) = your max budget

3) the exception
If you get the best flashes your manufacturer offers alongside with obtaining radio units, price becomes ridicous. You are essentially picking IR technology AND radio techonology since the upper tier flashes already have wireless built in.

expensive flash(es) + expensive radio(s) = past your max budget *

*unless you utterly need both IR and radio, you have not past your max budget.