I'd say a small shockwave movie would be your best bet. It would take what, about four renders with the pistons and the cheeses in different positions, and then just loop that and put it on your index page as the intro, then have an entry there for them to get into the main pages. the shockwave should be on a page of it's own, and kept as small as possible. The only other option you have is a gif, and that will lose all the 3d depth and color. Java, well, as a web designer, I don't care for java much except for forms and stuff. Java tricks just slow pages down and crash the browsers of at least half the people that will visit your page. I say shockwave, for sure.

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