compared to other companies' low end bikes trek has by far the best components, durability, and value. i sold and built trek bikes all summer and they do an extremely good job packing their $800 bikes with as much as they can offer. of course a cheaper bike won't be awesome and won't have a full XX build kit but it's all about how much money you can spend, and most steps of the way trek will be the highest quality of its class. bontrager makes perfectly decent stock components, and most low end trek mountain bikes come with hayes hydraulic brakes or avid bb5's. the only lacking area are the forks which are usually suuntor coil forks with shitty lockouts, but all other companies in that range are using the same ones
then you go up the line into the 100 series and they make some damn nice bikes. also not to mention the superfly which, aside from the front derailleur mount issues, is a super nice bike that weighs nothing
if you want to build it yourself from an underground company, go for it, but it's gonna cost you more than $1000