Just intercept the read and write calls! On linux you can just use 'strace $prog'; try it on a minimsal program that reads and writes a file. For a custom approach, this can be done with a library (using LD_PRELOAD). Plenty of articles about how to do this, e.g.
http://www.linuxjournal.com/node/7795 (essentially the same technique on Windows, or other OS with shared libs). Slightly more hardcore is to hook the kernel syscalls; not normally necessary (on linux this is effectively hooking the other side of glibc, where it talks to the kernel) but if all you've got a static binary it's one approach.
Note that all these techniques only show you the read and write calls made to the library/OS and - importantly - not what actually happens to the card. To see that, the next level down is to instrument the card driver to track the actual I/O operations (i.e. so you see what the card is really being asked to do, sans all the caching and buffering).
Note that's not the end of the story; there's what the hardware controller decides to do and when the hardware actually reads/writes the flash array. That's the level where the quality of the firmware in the controller(s) matters.