I'm teaching an undergraduate seminar in digital history this semester at the University of Mary Washington. The students in the seminar were shown an array of digital tools during the first 4 weeks of the semester. Of those, they chose a series of tools for their projects, and three of the four student groups in the course decided to use Omeka to create archives for their projects. [These projects, descriptions of which can be seen at the course blog noted above, include a site on civil rights leader James Farmer, a project using alumni interviews to tell the history of UMW, and a site exploring James Monroe's time as Minister to France.]
I should note that although I (via UMW's excellent Division of Teaching and Learning Technologies experts) presented Omeka to the students as one of many options, they all seemed to quickly get its possible uses as an archive and presentation tool.
We began with a test Omeka installation for the entire class with which all the students played around. Now, each group will have its own Omeka installation to begin this week to populate with photographs, scanned documents, and videos.
I'd be interested in hearing about how others are using Omeka in their own classes.