This tip may sound counter-intuitive but the simple reason your muscles are sore is because they are under-trained in recovery.
Think about it this way: Monday you do a lower body workout; Wednesday you do upper; and Friday you do some cardio. Your lower body works out for maybe 45 minutes on Monday and then basically stays still for an entire week. Week after week, your legs still become sore the following day.
Doing some extra leg work during the week would train the legs to recover faster. You see, muscle recovery works just like getting a tan. If you went tanning for 10 minutes once a week, you would probably burn, then get a little bit of a tan over the next months, but continue to burn as well. However, if you went tanning, 2 or 3 times a week, your body would adapt and start to glow! Just like how more tanning does not result in the burn, more training often times results in less muscle soreness.
Now I am not advocating tanning but this is a great way to understand muscular recovery. If you think that you could push yourself a little harder in the gym and are afraid of getting too sore, just remember that that soreness is temporary and will more thank likely be less of an issue than it was before.