According to back cover of the Dover edition, there are 150 illustrations in Principles of Art History. However, there are far more citations of works that are not illustrated. It has been my intention, as far as possible, to fill in the gaps.
To do this, I have made a few assumptions, which are entirely my own; you are very welcome to pick holes in them.

The web pages are intended to be 'read' with the text. As much of Wölfflin's argument depends on the simultaneous comparison of the formal qualities of several works, the relevant image appears every time that it is cited in the text.
Some of Wölfflin's key images therefore appear a number of times, next to the objects of his comparison. Hopefully, this will make his argument clearer.

Wölfflin spent a happy time as a student in Rome at the German Archaeological Institute. The picture was taken in Rome in 1886, when he was 22.

Subsequently, he taught at the universities of Basel (1893-1901), Berlin (1901-12), Munich (1912-24), and Zurich (1924-34) (biography), and his examples reflect this.
(If you are interested, here is a rough and ready zipped database in MS Access which will provide some summary data.)

It is, therefore, to the Alte Pinakothek in Munich, the Staatliche Museen in Berlin, the Kunsthistorisches Museum in Vienna and the Gemaldegalerie in Dresden that I have first turned in cases where the text reference is less than explicit. If I drew a blank, I searched other collections in Germany, followed by Holland, Saint Petersburg and London.

As prints generally exist in multiple copies, I have used any available reproduction. The Fine Arts Museums of San Francisco have a particularly impressive collection.

References that eluded me totally are listed here; I would be very grateful if anyone can help (email).

Invaluable background information came from Heinrich Wolfflin: An Intellectual Biography (1981), a PhD thesis by Joan Goldhammer Hart which is available from UMI ProQuest. A useful essay (Acrobat file 2.8mb) by Ms. Hart was published in the Art Journal in 1982.