John deposits $15,000 cash into his business account.

Later in the day (at another branch), there was $100 cash deposited into the personal checking account which is owned by John and Jane. The bank does not know who deposited the $100 cash.

How would you fill out the CTR for this?

I'm assuming you've read FAQ #27?

http://www.fincen.gov/whatsnew/html/ctr_faqs.html

(Sorry, I don't have an answer for you outside of that link)

I don't think FAQ #27 applies to this situation

The business account...is it a DBA, corporation, LLC, partnership...?

I think the question pivots on whether the bank should assume that John made the $100 deposit, which would require that it be aggregated due to his having completed the business deposit as well.

Has anyone tried asking the teller who took the $100 deposit?

I agree, but if the business is a DBA, then the $100 will have to be aggregated whether John made the deposit or not. If the business is a corporation and Jane deposited the $100, then the deposit would not have to be aggregated.

The business is a corporation.

Teller does not remember who deposited the $100 cash.