I have a few that I recomend, some of which have been mentioned before.
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Sac State, Sacramento California; A short jaunt across the footbridge over the american river and then you are connected to the American River Trail. Every type of running imaginable are avalible. I trained for my fastest marathon off of those trails.
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UC Santa Cruz;Lots and lots of redwoods. A very pretty area and some of the best running that I have ever done.
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McMaster, Hamilton, Ontario, Canada; there is a medium nature area near campus and lots of deer can be seen.
McGill in Montreal. Awesome. Lots of trails on Mont Real with some decent hills, a historic urban centre, and a great downtown. Excellent place to run if you can last the winters.