There’s actually quite a bit of Pierre Duhem’s work available online; but it is very scattered. A number are available through Google Books.
One limitation of Google Books, of course, is that Google Books entries are not universally available; in some countries Google imposes an arbitrary cut-off on visibility in order to avoid any potential copyright litigation. So it’s worthwhile to have other sources. Internet Archive has a number of Duhem’s works, tending heavily to Duhem’s physics textbooks.
Alain Blachair has an excellent website with a number of significant French-language works in philosophy of science, including several by Duhem.
And the Gallica digital library, of course, has quite a few, and, while I haven’t made a rigorous survey, it seems to include most and perhaps all of Duhem’s published work.
In addition, Duhem wrote several essays on scientific subjects for the 1911 Catholic Encyclopedia. Most of them are fairly minor biographical articles on various medieval thinkers relevant to the history of science (although the Oresme and Albert of Saxony articles are worth a quick read despite their short length), but the History of Physics article is somewhat more substantial, and is worth reading if for no other reason than that it provides an interesting early-twentieth century perspective on the history of physics by perhaps the foremost historian of physics of the day.
Let me know if you know of any others.