When it comes to the nerve center of a home theater, most consumers opt for an A/V receiver, which combines a preamp/processor (pre/pro) and multichannel power amp in one chassis. However, some enthusiasts choose to buy a separate pre/pro and power amp, believing that this results in superior sound quality, though it's generally a more expensive way to go. If you want the best possible sound—and you have the budget—you're probably shopping for separates.
Once you decide that you want separates rather an A/V receiver, you've crossed over into the world of high-end home-theater electronics, and you probably won't find these products at your local big-box chain. Specialty retailers provide the best selection, overall knowledge, and customer service for this type of product.
Don't get too hung up on specifications. You will find almost identical technical specs among various brands, making it virtually impossible to choose based on this alone—not that you'd ever want to choose an A/V product based solely on specs. Performance and engineering have reached a level of sophistication that specs such as frequency response, noise, and distortion are all more than acceptable in virtually every case.
Even when there are slight variations in the technical measurements, most folks would be hard pressed to detect any difference in a subjective listening test. There simply aren't huge discrepancies in sound quality from one manufacturer to another. However, there are subtle differences in the sonic signature of various pre/pros that is affected by the speakers and amps used, which is why it's important to use the same components when comparing pre/pros.
Having said all that, some specs—for example, the number and type of inputs and outputs—will help you to narrow your choices. For instance, how many source devices do you have? Do you expect to add more in the near future? Select a pre/pro with enough HDMI and other inputs to accommodate your current system and future plans. If you have an analog turntable, make sure the pre/pro has a phono input suitable for the type of cartridge you use (moving magnet or moving coil) unless you use an outboard phono preamp. Also, be sure the HDMI connections are version 1.4, which allows the use of 3D components, Audio Return Channel, and other features.
Some pre/pros offer balanced analog-audio outputs. Balanced connections minimize noise pickup in long cables, but in most systems, the cables connecting the pre/pro to the power amp will be very short, so this is not of critical concern. If it is to you, make sure the power amp you plan to use has balanced inputs.
Since pre/pros fall squarely in the high-end category, virtually all current models will meet your basic needs with certain features, such as the ability to decode all modern surround formats like Dolby TrueHD and DTS-HD Master Audio, automatic room calibration, video upconversion for analog video sources, and onscreen display via HDMI. (If a pre/pro lacks any of these features, look elsewhere.) Many manufacturers implement the auto-calibration system from Audyssey or Trinnov to provide setup assistance and room equalization (if desired), but others use their own proprietary system.
To evaluate the performance of a pre/pro's video processor, take a test disc to the retailer; Spears and Munsil's High-Definition Benchmark Blu-ray includes some good tests of the processor's deinterlacing capabilities, but my favorite processor test discs are the HQV Benchmark 2.0 Blu-ray and standard-def DVD, which can be ordered here. Familiarize yourself with the tests before you go to the store, then be sure the disc player is set to output 1080i (for Blu-ray) or 480i (for DVD) and run the tests to see how well the pre/pro's processor handles them.
Most pre/pros are sure to meet your needs; the key differences for most buyers will be the features. For instance, Marantz and Denon have adopted Apple's AirPlay, allowing you to play music wirelessly from any Apple iDevice through your sound system, while Integra offers 4K video upscaling. Ultimately, you will make your final decision based on the feature set that appeals to you the most—and, of course, the sonic character you find most pleasing with your system.
In fact, you might want to consider getting a pre/pro and matching power amp from the same manufacturer. Not only will they be sonically matched and optimized for each other, they will present a unified visual appearance, if that's important to you.
Hometheater.com has even more info if all this was not enough for you.