I agree with shootist's remark about companies like Benchmade and Spyderco driving each other to better performance. Both companies are leaders in the cutler industry without a doubt.
Spyderco's firsts are presumeably well-known to this board, but include the integral clip, round hole, popularization of zytel handles, custom collaboration, etc.
Benchmade has popularized some very important features as well. Their launch of the CQC7 & AFCK is what exploded the tactical folder crazy among production companies, they are the ones who got companies looking at non-stainless-steels for folders again, they are the ones who made all folder companies re-think their high-end locks. Benchmade had some firsts, and just as importantly, they took some good ideas and productized them right to really explode the market.
I try not to think in terms of what is my favorite company, as this can lead to accepting a product from a favored company that I wouldn't from another. Although it's almost impossible, I try to judge each knife on its own terms. Among production companies, it's Spyderco and Benchmade who have the most products that I like, and in my view, they are constantly leapfrogging each other in terms of knife design and feature leadership.