I'd guess by having a quality product with good design. Time tracking is definitely over-saturated, but Freckle is a simple, powerful product with great design. That makes it makes it much easier to stand out.
_neil is right. Freckle is simple (you can track time without the hassle of creating a project) and powerful (the multiple ways you can see your data is awesome, especially the "pulse" screen) with great design (its very pretty). That said, there's more features I'd love to see, but they are constantly improving the product, so its only a matter of time.
If you (or, okay, I) can create a new product which has certain selling points, and gain quite a lot of customers, how is the market still considered "over-saturated"?
I make my living exclusively in "over-saturated" or "nobody will pay for that" markets. Which so far has worked out just fantastically.
My first foray into an "over-saturated" market was a Mac news, opinion & tutorial site back in the late 90s. Every single person I talked to said the market was over-saturated, that nobody would read it & more importantly, I wouldn't get any advertisers. They were all wrong.