The Fourier Transform has many applications and you can find it in many places of maths and physics.
I will show a pair of well-know examples; in Quantum Mechanics, the position space and the momentum space are linked by a Fourier Transform:
$$\Psi(\vec{r},t)=\frac{1}{(2\pi \hbar)^{3/2}}\int_{\mathbb{R}^3} e^{i\vec{p}\cdot\vec{r}/\hbar}\Phi(\vec{p},t)d\vec{p}$$
$$\Phi(\vec{p},t)=\frac{1}{(2\pi \hbar)^{3/2}}\int_{\mathbb{R}^3} e^{-i\vec{p}\cdot\vec{r}/\hbar}\Psi(\vec{r},t)d\vec{r}$$
You can see that this is, in fact, a way to change the basis we are using.
Also, in optics, it can be used in coherence theory and in diffraction. Here's an example of a calculus of a coherence factor, which is the FT of the intensity received on a plane (with coordinates $\xi,\eta$):
$$\gamma _{12}(t=0,x,y) = \frac{\int _{S}I(\xi,\eta)e^{ik\left(\xi x /R-\eta y/R\right)}d\xi d\eta}{\int _{S}I(\xi,\eta)d\xi d\eta}$$
Fourier Transform is in fact very important in optics, and as I've said it is used in coherence theory and diffraction.
And of course, the application to change to frequency domain is really useful. Also, it can be used to solve some differential partial differential equations (incluided Maxwell equations in dielectric media, using frequency-time change).
Hope the examples are useful =)
PS. As someone pointed out in the comment, the FT is not linked with Heisenberg Uncertainty Principle. When applied to waves, FT shows that you can't have a 100% monochromatic wave -you must have a $\Delta \omega$ width.