shirt: in the desert, long-sleeve white Patagonia Cap. 1. great shirt. I found even high-end wool to be a tad itchy--may be just my mind at work. The shirt didn't retain stink very much at all. I am not very sweaty so that helped. After the desert switched to blue Patagonia cap. 2 longsleeve. great shirt, lasted the rest of the way. no holes, low stink, no itch.
underwear: Ex Officio boxer briefs. Wow these were awesome--I will probably use them for travel now. Great wicking, low stink, quick dry. a little $$ but absolutely worth it.
pants. long convertible Columbia Titanium. Wore them every day and they looked great. no holes, quick dry, dirt washed out well. I liked all the pockets. I was often accused of being too clean to be a thru-hiker.
camp shorts--nylon soccer/running shorts.
socks--Injinji (five toed), three pair. never had a between-toe blister, but these are a little expensive and would often get holes in under a week (ball or heel). If I had no toe blister problems, I would switch to cheaper nylon socks. I just wore the Injinjis while hiking, nothing over them. I had a short length pair of wool socks for sleeping.
shoes: New Balance 1063, then NB 760. Both were just regular running shoes, not trail runners. Not water-proof. great shoes, went through four pairs. They never fell apart structurally, I just had to get new ones when the tread wore out. Each pair lasted 600-700 miles. I didn't really have trouble with traction on the snow. On the steep passes/traverses, there were usually footprints to step in. they would dry during lunch hour if it was sunny.
I wore silk sun gloves (I don't like sunblock lotion) and a straw Stetson cowboy hat w/ a bandana to cover my neck. the Stetson was a good choice, it mostly held its shape throughout the whole trip. It also kept the rain out of my face (except for very heavy rains).
Rain gear. GoLite Virga jacket, el cheapo campmor rain pants. I only got the rain pants for Washington, not needed before that IMO. I wore them mainly in cold rains. They also doubled as an extra night layer when it got cold. I had Patagonia cap. 2 long johns for the Sierras, but nowhere else. I preferred the rain paints for a second leg layer in Washington, b/c they did double duty.
The Virga did ok, of course in a heavy rain, or when sweating, you get wet anyway. I wouldn't care too much which rain jacket I took in the future, I think they all work ok in light rain. And in a heavy rain you get wet anyway. I've never tried a $300 rain jacket though, maybe they do keep you dry in a heavy sustained rain.
Early on I just had a Marmot Dri-Clime windshirt. Very good product, very warm for its weight, but I would change it for another thru-hike. It was too warm to hike in, not warm enough for the cold nights. I did not have a puffy jacket. in WA I added a cheapo fleece.
I think next time I would just go: hike in longsleeve shirt, carry very light fleece, light rain jacket, and puffy down jacket (at least until WA, where I might switch the down to synthetic).
I had cheapo light fleece gloves, in the future I will get thicker ones. My hands were often cold in the morning. I wore plastic bags over my gloves in the cold WA rain, if I had the $$ I might get rain mittens next time.
my Serius fleece hat was great. built-in neck cover if needed in cold wind.