Hey, I've been riding a Trek Soho S for about a year now, and this summer, I'm looking into putting some money into it. It's still mostly stock, with a few exceptions. I bought it without really doing my homework, and it's served me well, but I've realized most of the stock components are ****. I'm specifically looking into replacing the pedals and handlebars (mostly for cosmetic reasons- silly, I know) but looking for other suggestions as well. I really don't know a ton about bikes (my friend who's a bike nerd will be helping me out) so I'd appreciate as much detail as you're willing to provide. I'm a student and use it pretty exclusively for my commute. Thanks for the advice.

handlebars:
i believe your bike comes with straight bars, so you're other options for multiple hand positions are: drop bars, bullhorns, and mustache bars. Riser handlebars could be an option too, but they don't provide multiple hand positions, and aesthetically don't differ tons from your stock flats. You also could trim down your stock bars if you feel they're too wide.

pedals: many people around here, myself included, are a fan of the MKS line. Personally I like MKS GR-9s, which are a bit platform-ish, and feel good with softer-soled shoes.

YES. The first things I replaced on my Soho S were pedals and handlebars.

Just get pedals that aren't complete garbage like the Soho's. If you're running the bike primarily fixed gear, I might look into shorter cranks. But that's only if you're on the smaller side. As a short guy who rode the small size, I'd get tons of pedal strike with the stock 170mm cranks. Kind of stupid to put 170's on a frame that has a bit lower of a bottom bracket than most fixed gears. Other than that, you can go up from there. The wheels however lasted me a long time, and put up with a lot.

But I like the Soho S. It gets a bad rap, but it has a special place in my ssfg heart.

Yup, pedals and Handlebars are the things that bugged me most about mine. I'm currently rolling Tioga Surefoot 8 pedals and a Soma Sparrow handlebar. I'd take exception to the statement that components other than the pedals are crap. The pedals are crap, I always felt like my feet were going to roll off of them.

I also went with shorter cranks... because I've got shortish legs.

Realize, I've actually changes a number of other things, but those were simply for how I ride (it's my daily-ish office commuter). Smaller chainring, fatter tires... haven't replaced any of the major mechanical bits that someone might call crap (headset, wheels, BB, chain, freewheel).