The first question I would ask is where do you live? If you live somewhere like San Francisco with a really mild climate, I would just look for a road bike with rack mounts on the frame. If you live somewhere that gets snow, I would look for something that can mount at least 35mm wide tires so you can swap studded tires on in the snow and ice (cyclocross, hybrid, or mountain bike fits this category). Then, to address ergonomics and riding position, go a bike shop and test ride different types of bike and see what feels comfortable. Some people hate drop bar road bikes, some people don't like flat bar hybrids and mountain bikes. Just depends on what you feel comfortable riding. Clothing is going to depend on the climate where you live. Around here, running gear will only keep you warm from early May until about mid-September; whereas in southern Texas, that would be more than enough for winter commuting.