
The first, and probably most important issue, is where you have your speakers. This takes two parts - where they are in the room, and where they are in relation to your sitting position. It can sometimes be difficult to move your speakers too much, as you might need to move your whole desk and kit too, but it's worth trying, as it can make a world of difference.
We'll try not to get too heavily into acoustics in here, but you need to understand the idea of "room modes". These are basically resonant frequencies, which in simple terms means that some frequencies sound louder than others, while others can be cancelled out. It's mainly noticeable in sub bass and frequencies up to around 250Hz, and it happens when the wavelength of a sound is an exact multiple of one of the dimensions of your room. The thing with room modes, however, is that the effects vary depending on the placement of the speaker and the listener. Try it - play some bassy music and walk around your room, and see how the bass gets louder and quieter. You'll probably find it's loudest near walls and in the corners.
This works the same if you move the speakers, too. So the primary thing is to avoid putting your monitors in a corner, or too close to the walls, as this will exaggerate those particular frequencies that your room already emphasises. Pull them in towards the centre and it will already sound more balanced. You also need to have the speakers at roughly head-height (when sitting down!), and in the classic "equilateral triangle" arrangement - so that your head and the two speakers form a triangle, to give the best impression of stereo spread, and to avoid phasing issues.

It's also common to try and place the speakers along the longest wall of the room – as this will keep side-wall reflections to a minimum, and thus won't interfere too much with your stereo image.
There are plenty of other issues caused by reflections and phasing though, and some of them aren't immediately obvious. For instance, if you have your speakers on a desk or table, then there can often be a flat space of hard wood right in front of them. This will reflect sound back up off the table towards you, which will make things sound harsher and more full of high frequencies. If possible, therefore, you should have your monitors on dedicated stands – which will also remove the likelihood of your desk resonating and adding to a boomy sound.
Hard walls can cause similar issues; not only can reflections be harsh and trebly, but they can also cause a "ring" (basically a rapid and high frequency echo). The classic way to test for this is simply to clap your hands and see how the sound dies away. If it rings noticeably, you'll probably need to do something about it. The good news is, that many rooms are set up to avoid this already - if you work out of a bedroom, then the curtains, carpets and bed will absorb plenty of high frequency sound already. If you're in a box-room or similar, then make sure there's a carpet down, at least. A sofa in the corner will help, and after that, you can start thinking about acoustic foam (the modern version of egg-boxes!). Try placing this absorbent stuff behind the speakers, on the ceiling above, perhaps to the left and right of your sitting position, and on any particularly reflective surfaces (painted brickwork is a killer, for instance).
So, how do you know when you've got all this set up properly? Start by making a test on your DAW - get a sine wave, and just make it play up the semitones from (say) C1. Listen out for any notes that are louder than others, or any that are much quieter. If there are dramatic differences, try tweaking your speaker position again. Once you've done this, listen to some commercially recorded music and see if it sounds balanced, the stereo image sounds good, and so on.
