First, offset the "levels" with commas or parentheses:

Sales by Store (by Day)

or

Sales by Store, by Day

If you are asking about the order, I think the correct order would be innermost to outermost grouping, but I cannot cite any authority for that, just experience.

Sales by Day, by Store

Looking at your two single-level examples (Sales by Day and Sales by Store), the Sales (numbers) appear on the right side, and the ordering qualifier appears to the left. So for consistency, I think I would continue that trend.

In your final example, sales are furthest to the right, then days, then stores - so I would title the report Sales by Day, by Store.

In all fairness, however, I could probably convince myself the other way too. As long as the labels of the qualifiers are clear, I don't think the title will lead to any confusion.

(edited to take @JeffSahol's excellent suggestion of offsetting by commas)

I would replace one of your by with per:

Sales by Day per Store

Sales per Day by Store

In this context by and per are effectively synonymous, so you can use either variant. However, for consistency's sake you should probably use per consistently in one half of the formula or the other, so that you always say (for example) Sales Per Day, whether or not the store breakdown is given.

Since the way you've grouped the data

It should say

Sales by Store by Day

or even better

Daily Sales by Store

Hope that helps!!!

I take these results are from an SQL query. You don't get to choose which way it is written, as it has to follow the sequence of grouping in the SQL query. The grouping by sales then by day gives different results than grouping first by day then by sales.