There's a special place called Kibune outside of Kyoto, approximately 2 hours travel or so, you need to change services a few times, but it is well worth it.
One of the trains is also a 'view train', large glass viewing panels to look out of, as the train ride is extremely scenic. There's a mountain/hill hike up to a temple and back down to the other side to the town. The town is situated on a water in a gorge basically along 1 single street essentially.
Restaurants are actually on the water fall and open facing it on tatami mats (these are very expensive to eat at, there's cafes literally next door not on the waterfall on otherside of road that are not expensive). It is a rather special place all round. There is a travel guide here, doesn't really do it justice
http://wikitravel.org/en/Kurama
Here's what the street looks like, this is about summer time. Autumn time it'd be all red.
Unfinished restaurant
Also Inari Fushimi Taisha is right next to a city station, and may be 'over done' but it is a great visit, and is open all night so you can do night photos in there. It's a touristy temple worth visiting, it's free and extremely accessible, and it looks fantastic. There is not many people there at night in summer (at least late night, I got the last train back).
Nara is nearby and is worth a half day trip (about 40 min from Kyoto iirc) if you'd like to take some photos of the tame deer in town right up close (they'll eat out of your hand). If you're patient you can edge closer to the baby deer within a few metres without making them run off.
There's another special place called Takeda castle (castle ruins). Most people will climb/hike the mountain up to Takeda itself, which I did and was a mistake. I realised afterwards, that ideally, you should hike an adjacent mountain to get a nice view of Takeda. If you're lucky there'll be clouds, which sit just below the castle ruins and make it look like it's floating in the clouds.
It is west from Osaka on the Shinkansen, and Himeji castle is about half way, which can be done in the same day.
I'm going back to Japan on a working holiday visa, but I wont be back there until September sadly.
If you ever have the chance to go to northern Japan, one of the most stunning temples I've been too is called Osorezan, it is near Hokkaido, it is in the Aomori prefecture, you have to get a train from Aomori to the end of the line around the coast line north and east to the peninsula, there is a bus a few times a day that goes right up to the temple ground.
It is rather stunning, stinks, but stunning. It is a strongly volcanic ground that looks like a barren wastle land, there is a lake which looks like a tropical beach at times. Apparently it is one of the three most sacred temples in Japans. Very ominous place. This place is known as the gateway to hell and for good reason. The temple itself is called Bodai-ji, wrong part of the country I know, but it goes overlooked.
Make sure to go to Dotonbori to eat in Osaka, there's also Izakaya for about 1200 yen for unlimited drinks for 1 hour if you're into that. And I believe Kobe is nearby to Osaka if you want to try some of the highest (And most expensive) rated beef.