Today, the prayers are written on ema, which are then hung on special places inside the shrine. The ema are usually beautifully decorated with various themes, from the shrine's crest (which are called Kigan-Ema) to zodiacs signs (Eto-Ema) or even... anime.
If during the old days only reach people afforded the horse donations, today an ema can be bought for 1000-1500 yen (12-18 US $) and almost all the shrines have racks with impressive numbers of ema.
This is the main ema rack from Meiji Jingu, beautifully built around one of the sacred camphor trees:
EXIF info:
Nikon D90
Lens: VR 18-55mm F/3.5-5.6G
Focal Length: 18mm
Aperture: F/5.6
Shutter Speed: 1/80s
ISO Sensitivity: ISO 320