Hi, Xudong,
In my experience, all cech stuff finally goes into the spectral sequence. To give more concrete examples in topology, Bott-Tu is the only resouce in my mind, e.g. to prove all cohomology theory coincide (singular, cech, de Rham), the defintion of euler class... To give more concrete examples in algebraic geometry, the basic example is the relation between Dolbeault cohomology and de Rham cohomology. Or compute the genus of P^1, elliptic curve by Cech. Or different interpretations of chern class of line bundles. Or Lefschetz (1,1) theorem. Most of these can be found in Griffiths-Harris.
Best,