I think that including the letter in some form or manner is a no brainer. The issue is how to do it, as some schools prohibit sending additional materials. All schools tend to have an optional essay where they ask you to submit any further information that is critical. At times there are word limits and clear instructions that this section is meant to deal with "red flags" (low gpa, loss of job..)If these restrictions do not apply for a given school, then this might be a potential place. You can of course make mention of it in your essays, and of course the dream would be for your CEO to send it on your behalf as a non reference supporting letter. These types of letters, if tastefully done, can indeed help your case. Email me if you want to get some more specifics on how to handle this.

Good Luck!

Alex