I havent had this problem yet with my C5, but previously I owned a 300ZX, and I applied conditioner to the seals at least 3X a year. Almost always took care of the rattles, except in extreme cold, when theyre going to rattle, regardless. In addition to removing the rattle, they never leaked!
I have had the same problem. There are two quick fixes I can recommend.
1. Figure out what side the rattle is coming from. My guess is that it is from one of the front latches. If this is the case you can try backing off the latch about and 1/8 to 1/4 inch from the full locked position. This adds just a little more pressure to keep the top tight. This worked on my 99 for awhile.
2. I bought a very thin single side foam tape from the hardware store (no more then an 1/8 inch thick). I traced a template of where the top sits on the front latches. From that cut the foam. I personaly like the look. The foam is black and hides any of the strach that might have been there from previous attempts of putting the top on.