In some towns outside of Tokyo you can use them in the buses. Look for those buses where you get a numbered ticket when you come in and deposit money into the machine based on your ticket number when you come out. Most of those don't care for the type of coin you use, so you can dump all your one yen coins there. Just make sure you count them beforehand so that you have the right amount for the fare.
Edit: Since it seems that some wouldn't believe this, here is a quote from Kyushu Sanko bus company website:
Q. Can I use 1 yen and 5 yen coins to pay the fare?
A. We can handle metallic currency that includes 1 and 5 yen coins. However, please aim at using no more than 20 coins at once, since it may cause the fare box to get stuck.
Similar source for Entetsu Bus:
"Is it possible to pay the bus fare with 1 and 5 yen coins?"
"Yes / We humbly accept your payment in such way"
My experience is that most local buses that have that kind of system are able to process one and five yen coins. I guess that it is because they function on an honour basis. That is, the machine is not actually counting the coins, so it can take anything.