How to organise large number of products?

Hi

i have nearly 100,000 "products" and the site is slowing down. I'm wondering about the benefits of using linked products - a lot of my products are the same but with different applications i.e. one product will be listed 20 times.

The only way i can think of reducing the number of products is to increase the number of categories. is this worth doing?

If i use categories names for the application data i can then link the products to the categories. but this would mean having a LOT of categories/subcats/subsubcat...

is zen cart able to handle this? any suggestions on another way to do this?

Thanks