Hands down, the most common name in shell material is Gore-Tex. It is also true that you will pay more money for the designer label. A decade ago, Gore-Tex was the only game in town for waterproof/breathable protection. Nowadays, there are
literally dozens of similar fabrics, such as Sympatex, Triple-Point Ceramic, Omni-Tech, and H20No Storm HB, that offer relatively similar performance. Rather than asking for a Gore-Tex jacket when you walk into the store, tell the clerk you are interested in a waterproof/breathable shell. Sure, Gore-Tex should be one of your options, but if it is the only thing you are shown, go to another store. Rather than sweat the manufacturer of the waterproof/breathable laminate or coating on the fabric, focus on features instead. Check for meticulously taped seams with no bumps or bubbles, perfect stitching, and a good fit.
The advantage of buying a Gore-Tex or Sympatex jacket is that both companies oblige the manufacturers who use these products to make sure the garments adhere to a minimum standard of performance. Because of these standards set by the makers of Gore-Tex and Sympatex, other companies follow suit and make sure that their garments have the same quality controls as well.
All waterproof/breathable jackets have durable water repellent (DWR) finishes, which eventually wear off. When this happens, you can apply products like Nikwax, ReviveX, or Zepel to restore the DWR finish. You'll know you have lost your DWR when the coat appears to be absorbing water. It is not the fault of the waterproof/breathable membrane (i.e. Gore-Tex or Sympatex) but the fact that the DWR finish is no longer causing water to bead on the fabric's surface.
Sorting out the drawbacks and advantages of three-ply versus two-ply shells is worse than the debate over whether Bill Clinton committed perjury. The systems work the same, and three-ply usually costs more. Two-ply jackets have a mesh lining, which adds weight, but may move easier when layered over fleece or wool. Three-ply shells are generally higher, and considered top-of-the-line, since the material is more expensive than two-ply.
Check the warranty of the jacket. Some companies, like The North Face, offer a lifetime warranty on the productyour lifetime, not the coat's. It's rare, but sometimes something can go wrong during the manufacturing of the fabric or coat. Make sure the company you are buying from guarantees the jacket will live up to its advertised performance.