Even when you do have a good reason to ignore them, you should still either disable that specific type of warning or, better yet, disable that specific warning for that specific spot in code using gcc's diagnostic pragmas [1].
I agree. This way you signal to other programmers reading the code that you were in fact aware of the warning and made a conscious decision to disregard it.
[1] http://gcc.gnu.org/onlinedocs/gcc-4.3.3/gcc/Diagnostic-Pragm...