From my understanding the expulsion decree applied to the Crown of Aragon and Castille, the future colonies would sort under Castille and jews thus remained forbidden to settle there, but what about other parts of the conglomerate monarchy? Did the expulsion decree extent to Sicily? What about later acquisitions like Naples, the Spanish Netherlands, etc.? What happened to existing jewish populations there?
That's a great question!
Actually, Sicily was included in the expulsion decree of 1492, signaling the end of a thousand years of Jewish life there. In a sense, it was something of collateral damage- the main reason given for the expulsion, that non-converted Jews were causing conversos to revert, was not a factor in Sicily, nor was a more minor factor of accusations of usury among Jews. Sardinia as well was also affected. However, the mechanisms and dates of the expulsion were different than in Spain proper; while the declaration was issues on June 18, 1492, with a three month window given to allow Jews and Christians to settle their affairs with each other, in the end the expulsion didn't truly go into effect until January 12 after a memorandum was brought to King Ferdinand, explaining the huge blow to the Sicilian economy which would result upon the Jews' expulsion.
At around the same time, there were also expulsion decrees in several other areas which, while not necessarily under Spanish control directly, were able to be influenced by it. For example, there were expulsion decrees in Milan, Parma, Portugal, Navarre, Naples, and Provence between 1480-1510. However, not all of these were carried out; for example, in Naples the ruler refused to enforce any decree to expel the Jews and in fact accepted many of the Jews who left Sicily and Sardinia, with nothing carried out until 1541. The same seems to have been true in Milan. In Spanish-controlled North Africa, Jews were never expelled at all.
(Open) Jews were not permitted in the Spanish Netherlands. The major Jewish communities in the Netherlands, particularly Amsterdam, only came to be decades after the formation of the Dutch Republic. The Spanish government was very insistent on this; when the governor of Brussels wanted to fill his coffers by accepting money in return for permission to establish a Jewish community and synagogue near Antwerp, the Spanish crown completely forbade the deal and banned any members of the government in Spanish Netherlands from even considering it.
It should be mentioned also, though, that "expulsion" didn't necessarily mean "all Jews left." In many cases, it simply meant that Jews converted to Christianity in order to remain or even to return, which large numbers of them did. Some of these converted Jews maintained crypto-Judaism, at least initially; others did not. Some later reverted to Judaism. To go back to the topic of the Spanish Netherlands, once the major communities in the Dutch Republic were established, many conversos there took the opportunity to move across the border to Amsterdam and revert to Judaism, for a variety of reasons spiritual, economic and political (particularly as the Dutch Republic became more powerful and Spain less).
Sources:
Simonsohn, Between Scylla and Charybdis: The Jews of Sicily
Kamen, "The Mediterranean and the Expulsion of Spanish Jews in 1492"
Israel, "Spain and the Dutch Sephardim, 1609-1660"