It'll directly affect you physically, and if things are not right it'll be painful. The room itself is often not too difficult to make sure is ok. I prefer having it not too hot in the room, and I like having a good circulation of air. An open window may be good if the season allows it. I haven't worked a lot with this though, at home things are very ok as they are.
Next thing is furniture.
I had some serious problems with pain in my lower back a while ago, and they went away when I got myself a new chair. Good support for the thighs and the back, as well as elbow pads helped. The chair I have now costs approx 1000 USD, but it's the best chair I've seen. Biggest advantage of such a chair is the good possibilities of adjustment, something I found to be useful. I have also got a table for my monitor, keyboard and mouse.