Places with just a few cafes and streets seen in the anime aren't worth the trip.
Something like nature from Yamanashi (Yuru Camp) or Oarai for the tank festival (Girls Und Panzer) would be fun.
I should write up my explorations sometime as I think it was more detailed than any of the ones I can quickly find on Google in English, e.g. going out to the Keage Incline. It was a great excuse to wander around Kyoto, a great city.
While I'm talking about the Kyoto area and anime, I've got to add that if you've seen Chihayafuru, go to Omi Jingu (近江神宮). Otsu is right there and Lake Biwa is neat anyway. I was able to watch some live karuta, chat about the show and the game, buy some cards and very poorly attempt to play with them (sorry, haven't actually memorized 百人一首 yet!).
i actually visited sendai for haikyuu! i enjoyed my time there a lot - there's a lot of beautiful day trips available like matsushima and yamagata - but i wouldn't recommend visiting it for haikyuu. sports stadiums are not that interesting from outside and most of the actual locations in the manga are based on a small town deep in the countryside.