Do you mean paradoxes as in "surprising but correct predictions of a theory" (like time dilation), or paradoxes as in "logical inconsistencies caused by incorrect calculations that look correct to a novice" (like the twin paradox)?
If you are particularly interested in paradoxes in QM, see also the review http://xxx.lanl.gov/abs/quant-ph/0209123 [American Journal of Physics 69 (2001) 655 - 701]