Primacoustic's Recoil Stabilizers as shown on the left, or relatively cheaply with some open cell (closed-cell will work too) neoprene, or even some mouse pads.
So why is this so important? When a speaker is sitting directly on a desk, console or speaker stand, the low frequencies radiate through the wood or metal faster than through the air. This means that those frequencies either get to your ear first that way, or you can feel the vibrations before you can hear them. Unless the two occur at exactly the same time, there's some difference in phase, which can result in a subtle yet very real blurring of the sound. As a result, it will be just a little harder to hear your low end distinctly, which makes it more difficult to EQ.
Decoupling those subwoofers from the floor can really help too. While sometimes the coupling with the floor can make your low end feel bigger, it will be a lot clearer and distinct if decoupled. Aurelex even has a product for this called the SubDude HD, although you can probably put together a DIY setup that can work just as well.
Regardless of the brand, model and type of speakers that you use, decoupling is a cheap and easy way to improve your sound right away. Give it a try.