If you have too many categories, then you have to think carefully:
1. Are all of them necessary?
2. Can you combine some categories which dont have too many products?
3. Can you move some categories into some other categories, make them sub categories?
You can use fly-out categories if you have multiple levels of categories.
I happened to stumble upon a very good SEO post about site navigation which I did a summarize and put into Zencart's context here:
http://blog.rubikintegration.com/200...s-of-products/
Hope it helps,
Raine