Garner's Modern American Usage has this on nested parentheses under an entry for square brackets ([ ]):
brackets often show parentheses within parentheses
Smith and her commander (Robert Parnell, also a [helicopter] pilot) both survived the crash.
But in some fields, such as law, it's not only acceptable, but customary to use parentheses within parentheses.
For what it's worth, he also has this on the use of parentheses:
Virtually any punctuation mark is subject to an annoying overuse, but this is especially true of parentheses, which to be effective must be used sparingly. When they appear at all frequently, they tire the reader's eye, add to the burden of decoding, and deaden the reader's interest. Sentences can sag with all the qualifying parentheticals.