Customer wants to deposit a credit card check which we always put a case by case hold on. She has a $200 credit card check and a $600 credit card check. She wants to put $500 in her personal account and $300 in her business account. Do we have to make $100 available in each account?

No. Only $100 from total day's check deposits.

...assuming her business is a sole proprietorship and is, thus, the same customer.

Some banks simply refuse to accept credit card checks for deposit and point out that the customer can obtain a cash advance if there is credit available on the card. (Yes, the interest rate may be higher and interest will begin to accrue immediately, but alas and alack, life is full of choices.) A case by case hold probably is not going to change your risk level at all.

So do I understand that if a customer makes 5 deposits throughout the same business day then we can hold the entire amount of those 5 deposits less $100? In other words, you only have to make $100 available one time during each business day?

For the same customer, yes. You are allowed to include all of Jane's check deposits including those she makes into her joint account with Jim.

I was confused by this as well, since the only reference in the Reg I could find to aggregating the day's total deposits was when using the Large Deposit Exception, not a case-by-case hold. However, the following verbiage is contained in the model notice when describing case-by-case holds, which implies the $100 availability is not per item (or type):

From the C-4 Model Notice (referring to deposits of local and non-local checks):

"If you deposit both categories of checks, $100 from the checks will be available on the first business day after the day of your deposit, not $100 from each category of check."

If a more clear cut answer can be found in the Reg I would appreciate the cite!

From Reg CC Commentary:
D. 229.10(c) Certain Check Deposits
5.c. A depositary bank may aggregate all local and nonlocal check deposits made by the customer on a given banking day for the purposes of the $100 next-day availability rule. Thus, if a customer has two accounts at the depositary bank, and on a particular banking day makes deposits to each account, $100 of the total deposited to the two accounts must be made available on the business day after deposit. Banks may aggregate deposits to individual and joint accounts for the purposes of this provision.

I think the regulation itself is very clear regarding aggregation and the $100 rule:

(vii) The lesser of--

(A) $100, or

(B) The aggregate amount deposited on any one banking day to all accounts of the customer by check or checks not subject to next-day availability under paragraphs (c)(1) (i) through (vi) of this section.

Thanks to everyone for their input. I understand it now.