Beyond the difference in construction and theoretical operation, they function pretty much the same in terms of performance for equivalent types of BJT. If you find a good spec'd NPN, chances are there is another equivalent PNP somewhere.
The 'general purpose' matched complimentary BJTs are NPN is 3904 and the PNP version 3906, similarly NPN 2222 and its complimentary PNP 2907.
Yes, you can substitute PNP for NPN by reversing the connections in the schematic, keeping track of the bias source and collector resistors to insure its placed properly. Make sure the output that feeds the input into the next stage is the proper polarity
or that the design doesn't consist of mix NPN and PNP together, for example push pull amplifiers.
Note, substitution are for general purpose transistor designs, such as using them as simple amplifiers or switches. Its uncommon today, but NPN or PNP specific designs do exists and are designed to optimize their performances, such circuits are easy to spot because they do not or are very restrictive about what BJT can be substituted into the design. In the amp sample, Q4 and Q5 are complimentary matched pairs like a 3904 and a 3906, substitute them at your risk.