Theme 'flavors' are variants of a theme &mdashl; an example might be having a different color palette but otherwise using the same layout, typography choices, etc.
You can develop distinct 'flavors' of your theme by working up a separate style sheet (CSS) and also notating the alternative flavor in your .info file.
As your original theme CSS will be loaded, with the flavor CSS after, the flavor CSS need only contain those declarations which should be different from the original. Often a flavor style sheet will only have a few lines, describing different background and text colors, etc.
Some designs demand conditional styles for IE only, while your theme may include a style sheet for IE, it's also possible that a particular theme flavor may require it's own conditional style sheet as well. (Most obvious case would be if you are using rgba in your design and need to replace that code with proprietary Microsoft filters.)