I use my staff shorts when I go hiking, even off of P2 property. The columbia shorts (cotton) were excellent (the ones sold in 98). The new columbia zip offs are pretty good too. These are made of supplex. They dry faster. I have also used cotton Carhartt shorts and been pretty happy with them.
Patagonia makes a popular short called the standup short. Good deep pockets and a nice cut. I've never used them myself but a number of people have sung their praises.
A type of short I would avoid is Umbros. They are not very durable. They are also slick and don't help your pack to stay up. The plus side is they are comfortable. I use them for sleep clothes.
Any T-shirt will do. I echo John's recomendation on the Duofold T-shirts. Made with Coolmax (which is polyester). Not a necessity, but makes it nice on those cool evenings sitting around the imaginary campfire.
This is a topic I'm not familiar with so someone chime in if you know about it. There are some travel shirts that advertise to be UV blocking. These tend to be nylon or polyester. Are cotton shirts UV protected?
Socks. People who use Smartwool swear by them, or as some people on this list refer to it, "are in love with them". I've never used them but I can't see shelling out $20 for a pair of socks. Thats just me. Most importantly you need to have wool socks. It is difficult to find 100% wool socks. Most hiking socks are about 80% wool with other materials mixed in. Just make sure there is no cotton in there.
To echo John's comments about "cotton kills". Just as guns don't kill people, people kill people; the same can line of thinking can be applied to cotton. The reason people say this is because it is not one of the more technical and best working materials out there. How many well informed backpackers wear blue jeans on the trail these? Not many. Doug Palmer told us that at one time people only wore synthetic materials, then cotton was the thing to wear, and now its moving back towards synthetic. Just a fad? I don't know but I save my cotton for wearing around here in this muggy MS climate.
If you go with 2 pairs of socks (the Smartwool people say they don't use 2) then make your thin inner sock either a coolmax (polyester) or silk material. People used to use Polypropelene (sp?) but those tend to be warmer than coolmax socks.
Goretex. Yeah, I've got Goretex, but I'm not completely sold on it. I've done my fair share of sweating in my goretex. Long days of hiking in the rain at Philmont and other places have left my clothing wet. Pit zips, venting, what ever, you still get wet. Goretex is an inactive membrane. If there is water on top of it, moisture won't evaporate out. That's why goretex is inside (or middle) and there is shell of nylon or some material on the outside. The outer shell must have a water repllant coating to keep the water from soaking in. If it is dry on top of the goretex, water will evaporate out.
There are a number of "breathable" products out there for raingear. I tried out the new Marmot Thunderstorm jacket this past year. I was reasonably happy with it. If it rains you are going to get wet. Breathable material breaths some, just don't expect to come out of a storm bone dry. Rain water won't get in, but your sweat may build up. This will especially be the case if you buy a cheap $20 rain jacket that does not label itself as being breathable.
The main reason you want a rain jacket it is to help keep you from getting hypothermic. Rain wear keeps you from being completely soaking wet and keeps that biting wind off. So do use it, just don't expect to be bone dry if you are humping a pack in the rain.
Warm stuff. Polar fleece is polar fleece. 200 or mid weight is the typical weight for Philmont's summer climate. Down jacket may be a bit much. Just don't use a college cotton sweatshirt. I'm sure you can find a good deal on fleece especially with spring and summer right around the corner. Higher price fleece is more durable. Then you get into the technical fleeces like windstopper. Windstopper fleece is excellent. I have one of these jackets myself and I really like it. Its expensive though.
You can do Philmont without going all out on buying expensive gear. I did it with an old Tshirt and old pair of shorts, non breathable raingear, no gaiters, and an old wornout rental pack I bought from Philmont on my trek. Its doable with out much extra stuff. There's just little things here and there that, for me, make the experience easier or more enjoyable. I got the backpacking equipment I use now from 1995-present getting things here and there, and on a college student budget at that.
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