After perusing some of the many Omeka-powered sites, here are my thoughts.
Oh my goodness, I am in love with this site: Treasures of the NYPL! The simple-yet-full front page is great; it shows some of the collection images (one of them links to A.A. Milne's original stuffed animals, which were the inspiration for Winnie the Pooh!) and lists the main categories of collections, all while taking up very little screen real estate. The user can then choose to explore the rest of the site as he pleases. (I also like the breakdown and simplicity of this site: Making the History of 1989: The Fall of Communism in Eastern Europe.)
The Short History of Seed and Nursery Catalogues in Europe & the U.S. also stuck with me, mostly again for its great homepage. However, I also like how the site is organized, in a format which looks almost like a term paper and displays items chronologically. I'm not certain we could necessarily do a chronological series for our own project, but perhaps we could break down the victim memorials (I believe Molly has already mentioned this, as well) by tower location, birthplace, age, or something else entirely. We could also randomly rotate photographs on the front page so that all of the people are represented equally.
And I like this final page, Bibliothèque Numérique - Université Rennes 2, not only because it's French (yes, I'm partial to that language), but because it makes use of a lot of great Omeka plugins. It's neat to see tagging being used on this site, as well as geolocation. Again, I'm not sure if we could use something like geolocation, but it's good to see as much as we can of what is out there, and then we can decide as a class what is important to include.
I have to admit (and you've likely noticed) that I'm a sucker for an aesthetically pleasing site. Of course, the content is extremely important, but I don't think many are going to want to look at, much less navigate, a site which isn't clean and user-friendly - no matter how full of information it is. Therefore, I tend to lean towards an emphasis on the visuals of the website, particularly those of the front page (so we can draw people further into the site!).