I write about sending invites that can be reused, or even saved because they are so lovely in my book Eco-Chic Weddings. Some ideas: seed packets with a bellyband for the invite, an ornament that can be hung on a tree. But, don't do anything tacky, like a magnet. Here are two ideas I really like from past issues of Martha Stewart Weddings:
Bookmarks

The bookmark idea is really for save the date, but I think you could just as easily turn this idea into your wedding invitation. I have always loved glassine envelopes (probably not too eco-friendly), but you could fill the envelopes your favorite {fair trade} tea, or locally harvested, or organic, dried lavendar. The envelopes pictured here have confetti, and are favors, but I think an invitation with the same idea would be sweet too.

And don't forget to use recycled materials!
When I was planning my 2005 wedding, and writing my book at the same time, I went to countless invitation web sites and combed the sites looking for recycled paper options, to no avail. Things are changing, behold Not From A Box Unique Invitations--they've just added a line of recycled paper...that doesn't have any seeds or petals in it ;)
More invitation ideas:
Handmade Paper
Recycled Invites
Tree Free