Here is the table of what happens when you cross any flower with any other flower, color-coded to help you visualize it. I have excluded the flowers that can only be found through mutation liquid or extinct seeds; if you would like to see those in the table, click here. (This table does not have Arthurium, Baccatus, Lilia, Tahitian, Tilia, or Venus.)

To use the table, look up one flower on the left column and the other in the top row. The place where they meet is the result of cross-breeding those two flowers. This table is useful for finding out the different ways to create a certain plant, as it shows every possible way to create those flowers.

One thing that surprised me in my research is that there is no way to create a spotted flower, and yet it is a common flower -- so, if you have a spotted flowered plant, make sure to self-pollinate it so that you will have spotted flowers to mix later on in the game. You can only get spotted flowers by buying them from the store (the common seeds) or from your original stash.