If you know audio, then you know that a subwoofer can actually make bass worse. Look at any recording studio and they use monitors, not 2 cheap tingy speakers with a big thundering sub.
Yes a cheap 2.0 setup will not sound good, and yes a subwoofer can make up for cheap speakers making a cheap 2.1 system sound better than it is. But I would advice you to get the best 2.0 system you can afford. M-Audio has quite a lineup and you can't go wrong with them. They have many awards under their belt.
There are also many other good 2.0 setups that would blow either of the 2 above systems out of the water. Headphones sound great and they don't have a subwoofer so think about it. Now if you were doing a surround home theatre then that is a different issue and you want a subwoofer for the LFE channel in movies. But even a decent home theatre uses 2 very nice tower speakers up front and when listening to music you use only those without the sub.
Also 2.0 monitors have an integrated amplifier that is designed to be neutral and not color the sound. It is of much higher quality than what is available in cheaper computer speakers and is one reason they will sound better. For under $500 and a nice set of speakers that will fit nicely on your computer desk, it's hard to argue against a pair of monitors and M-Audio are up there as some of the best. Their AV series are more affordable and more designed for computers. If you can swing it, step it up a notch into a real pair of pro audio studio monitors such as the M-Audio BX 5 Carbons. There are also other brands such as Emotiva, Audioengine, KEF, JBL, KRK, Dynaudio, etc....