Anything that relies upon users to consistently give it accurate data manually is doomed.
Doomed in what way? Commercial trackers like Freckle and Harvest are successful, growing businesses.
By this critereon, Excel is doomed. Whatever your definition for “doomed”, I disagree.
What’s the alternative for time-keeping applications?
Record what the user is doing.
I’ve had success doing the opposite. Rather than tracking how much time I’m spending on things, I timebox everything and use a timer to enforce it. It doesn’t work in every case, but it’s a nice way to keep focus, IME.
I started using the hamster time tracker some years ago and have been happy with it.