Goretex is by far the most reputable and "trusted" within the industry and amongst consumers, however there are at least a few excellent counterparts to Goretex, PARTICULARLY if you are price-conscious. As consumers, we should understand that high-recognition brands like Gore (Gore-Tex and Windstopper) charge premium prices because they CAN. That said, Gore-Tex is still probably the best product out there-- especially when it comes to breathability. Anybody can make a fabric waterproof-- that's easy and cheap.
Take, for example, Mountain Hardwear's Conduit product, used mostly on thinner, lightweight shells. I own a MH parka that uses Conduit technology and it is absolutely superb in terms of breathability, waterproof-ness, and comfort. I think it is considered a 3-ply waterproof system, and also has a 2-ply variant. There are many other similar 3-ply systems out there too.
I don't necessarily look for the Gore-Tex brand on my clothing and shoes, although it's always an added benefit (plus usually the most expensive). I trust an overall brand more-- so I'd buy a Patagonia, Cloudveil, Mountain Hardwear, etc jacket anyday, even without Gore-Tex. Many of these products have been reviewed in magazines like Outside and Backpacker.