So excited! My mom booked her ticket--this will be her first trip to Asia.

So we are looking at

April 7 - Osaka (twin room)
April 8-9 Kyoto/Otsu (single room for her, I will stay with a friend in Otsu)
April 10-13 Tokyo (twin room)

For Osaka, it looks like there are some pretty good rates on Expedia.

For Kyoto, I think I'd prefer to find her a room in Otsu as that's where I am staying, and she's a little nervous about being on her own. There are some okay places in Otsu on http://www.japanhotel.net (thanks for the suggestion). However, I don't know if they have availability. Most other sites show the budget hotels as being full booked.

For Tokyo I will start down LapLaps list and Tokyo Inns as suggested.

If anyone has any other ideas or places that I should be looking at, please let me know!