What would an use case scenario be like? I know that there's plenty information about this in the user manual, but i'm a beginner and don't know really how to handle that information. Thank you for your time.
Flash can always be used to put static assets for your application, including microblaze program, configuration options, image, sound, etc.
Most importantly, the fpga bitstream must resides on flash. All current xilinx fpgas are SRAM based and loose their content at poweroff. You need a non-volatile flash to store the bitstream, which is loaded at poweron automatically. Note that some fpga have internal non-volatile flash (notably, the Spartan-3AN). It only provides a convenient way to package the fpga and the flash together.
You may wonder why there are 3 different types of flash on the board, if they all do the same thing? While more memory is rarely bad, this is to allow the designer to try out different flash technology. This is a prototyping board after all, the 3 flashes have different interfaces and design tradeoffs, and having 3 is useful when someone want to try them out before implementing their own solution on a custom board.