Have you sorted out your guest book yet? Several people have done wonderful things with decks of cards, subway/movie/museum tickets on here, but you may like the idea of binding some homemade paper. There are tons of tutorials on here on how to make the paper... you could include petals from the flowers you intend to have in your bouquet or recycle the movie/concert tickets that you want to keep and just take up space and never get looked at in the very paper that your well wishes are in. You don't even need to bind it. Have everyone put their wishes into a treasure chest. You can get unfinished "treasure" chests at Michael's and add all the accoutrements yourself. The Booty of you wedding.
As for favors... my DH and I gave out handmade recipe books filled with the recipes of the food served at the reception as our favor. They were well received and have been referred to since, even by me.