I am currently developing a CUDA application that will most certainly be deployed on a GPU much better than mine. Given another GPU model, how can I estimate how much faster my algorithm will run on it?
You're going to have a difficult time, for a number of reasons:
Clock rate and memory speed only have a weak relationship to code speed, because there is a lot more going on under the hood (e.g., thread context switching) that gets improved/changed for almost all new hardware.
Caches have been added to new hardware (e.g., Fermi) and unless you model cache hit/miss rates, you'll have a tough time predicting how this will affect the speed.
Floating point performance in general is very dependent on model (e.g.: Tesla C2050 has better performance than the "top of the line" GTX-480).
Register usage per device can change for different devices, and this can also affect performance; occupancy will be affected in many cases.
Performance can be improved by targeting specific hardware, so even if your algorithm is perfect for your GPU, it could be better if you optimize it for the new hardware.
Now, that said, you can probably make some predictions if you run your app through one of the profilers (such as the NVIDIA Compute Profiler), and you look at your occupancy and your SM utilization. If your GPU has 2 SMs and the one you will eventually run on has 16 SMs, then you will almost certainly see an improvement, but not specifically because of that.
So, unfortunately, it isn't easy to make the type of predictions you want. If you're writing something open source, you could post the code and ask others to test it with newer hardware, but that isn't always an option.