Definitely don't use nofollow. Using nofollow won't solve the problem of having too many links, and will just end up hurting your site. It is almost never a good idea to use nofollow on internal links.
What you should consider instead is to have navigation that changes in response to what section of the site the user is in. For example, if the user is in the automotive category, it makes sense to have links to tires and oil, but it's not necessary to link to a subcategory for perfume. Having contextual navigation is great from an SEO perspective, and also provides for a better user experience of not overwhelming the user with a hundred choices.
That being said, limiting a site to having 100 links per page is a very old Google recommendation and is not a hard and fast rule. Having a lot of links on a page makes it more difficult for Google to crawl and dilutes the link juice on a page, but is sometimes necessary. Amazon.com, for example, has 300+ per page. How many links Google is willing to crawl is a factor of your site's Pagerank.