When I export an EPS file from Prism 5 Windows, an entire page gets exported (not just my graph or layout) so there are huge margins.

If you export to EPS format and choose to change the size (by choosing 'Make width..." ), Prism 5.00 and 5.01 export an entire page, so usually has lots of white space. If you keep the default, to export at the actual size, then Prism crops and only exports the graph itself (rather than the entire page). This glitch is fixed in Prism 5.02.