Hi Phil,
for Cyclone III designs, you can use Quartus 13.1 Web Edition without a license for everything including Signaltap. Only licensed IP, e.g. PCI compiler isn't available without a respective license. Most IP is contained in IP Base suite bundled with Quartus subspription license. Means if you have a recent Quartus license, it also enables licensed Quartus 13.1 features.
PCI compiler is legacy IP, I'm not sure if respective license (e.g. 6AF7 0022, 32-bit Master/Target) is still contained in IP Base suite or must be purchased seperately.
Regards
Frank