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Actually I search this for my father: he uses some old (2000) software (Sobotta made by Elsevier). It allows to add/remove layers of images containing different organs/systems.
It has nothing fancy like 3d graphic models or rotating the body. At extreme it could be done in javascript. It should be very simple to make such a thing, provided that you have the images. I found some materials on wikibooks.org ((a Wikimedia site), but they were incomplete and he was dissatisfied with it. Also internet access is a problem, so an offline library that could be updated from time to time would fit better than some site.
I almost forgot! It has to be in German language! Sobotta is in english if I remember correctly (probably there are at leat 2 CD versions). But why wuld you need it in german if everything is in latin anyway. I was also searching for linux med software but I wuld advise you to stick with microsoft for the time beeing. I ended up buying the Sobotta anatomy books - they are expensive but you'll need them basicaly all the time so I think it is a good investment (and you can probably sell them to 1-st year med students if you really want to - I didn't).
The KVocTrain program has some human anatomy flashcards in German. You can get it from the Ubuntu repositories, by going to the Applications menu Add/Remove Programs and searching for KVocTrain. Once you have it installed, if you go the File menu Get New Vocabularies, you will find a list that includes many medical and anatomy related topics. Then, just select the ones you want, and they will be downloaded and added. The Help button doesn't work when running in GNOME, but you can find a manual explaining how to run KVocTrain here: KVocTrain has worked fine for some language learning I've done, but the project has recently been renamed Parley and is being redesigned to improve its interface.
You can find out more about this at the KDE Education Project site mentioned above. JMemorize is also a good vocabulary learning program (with a more user-friendly interface), but I don't know if any pre-entered medical vocabularies are downloadable. Hope this helps!