So, I'm somewhat conflicted on the topic. I generally prefer a well-made boot that uses one-piece leather construction, a design that's inherently water resistant, especially when the boot is well cared for and treated with a waterproofing agent like Nikwax. Better still is a boot with a true leather lining, something that's rare these days. Granted, this isn't to do with waterproofing but the boot's fita leather lining molds itself to the wearer's foot for a custom fit. Most boots today use Cambrelle, a fabric that works very well because it's comfortable right out of the box. The Baffin ($230; www.lowaboots.com), though, employs leather lining.
Having said that, I think that in areas where wet weather and minor stream crossings are a given, the Gore-Tex lining probably makes some sense. And some fine boots use it at a reasonable priceL.L. Bean's Cresta Leather Hikers, which have a Gore-Tex bootie, sell for the eminently reasonable price of $169.