This question has come up a couple of times in the past month or two. Larry Stein, the resident dental authority, has expressed skepticism about this in a couple of threads, including this one:
http://www.scubaboard.com/showthread.php?s=&threadid=29092
Having dealt with fairly regular issues with sinuses and ear clearing as a freediver and occasional scuba diver, I tried one product (Clear-Ease) that contains papaya and pineapple enzymes. After giving it a fair tryout, I have to admit that I could perceive no difference between when I used it and I didn't. Based in part on Larry's concerns about the potential effects on the tissues of the mouth (it's chemically similar to meat tenderizer), I discontinued using it.
I've found that the biggest aid to having clear sinuses and being able to equalize for me personally has been to rinse saltwater through my nasal passages daily. There are different ways to do this with squeeze bottles or special pots.
A lot of my friends get help from steroid sprays such as Flonase, Nasonex or Nasarel. These all require prescriptions. I tried this but had to discontinue it because it was causing thinning of my nasal tissues and potentially could have led to bleeding. Allergies can also cause difficulties with sinuses and equalizing.
The only medication I've found that has made a big difference to me personally is Afrin, a spray decongestant, used a half hour or so before diving. You have to be very careful with this, though; it shouldn't be used more than three days running, has a rebound effect and can lead to habituation. If it wears off during a dive you can get a reverse squeeze upon ascent.
Also, remember to be very gentle when attempting to equalize. "Clear early and often" is the mantra; don't wait until your ears feel pressured as you descend. Trying to equalize forcefully can cause serious, permanent damage (I have one friend who became deaf in one ear when he blew out a fragile ear structure called the round window while trying to equalize vigorously about 10 years ago).
Finally, if you have issues with your ears on a regular basis, you ought to see an ear-nose-throat doctor. What works for one person often won't work for another.
I'm not a medical professional, just another diver, so I'm just sharing my personal experience for informational purposes. Good luck!