One of the most beautiful place to temple lodging is Koyasan which is close to Kyoto. Different temples offer lodging with a traditional meal included. They also offer the opportunity to pray with the monks early in the morning (5 a.m.) and before dinner.
In order to reach Koyasan from Kyoto you have to take a train to Osaka (Namba station) and from there take another train Nankai Koya to Gokurakubashi and finally take a spectacular cable car to the mount :-) It's quite a trip but I belive it's totally worth it.
I went there this summer and it was a really awesome, especially the graveyard. Temple lodging in Koyasan it's quite expensive (around 14000 yen each) tho. They ask you to book one week in advance, at least, but I manage to get there with a one day notice by asking the hostel's staff in Kyoto to call them, usually if someone can speak Japanese it's far easier to overcome these little problems :-)
You may also wanto to visit the Official tourism site