The University of Rochester Libraries has a Web site, “Lincoln and His Circle”, available at http://www.library.rochester.edu/index.cfm?page=379#”. At the moment the site is more of an index-with-images of letters that were written to/from Lincoln, but 26 of them have been transcribed and there’s a promise of more transcriptions over time.
You can browse the letters by writer or recipient, or go through them by date. You can also search by keyword. A search for emancipation found five results, with three of them written to, and one written from, Abraham Lincoln. (The other one was written from JL Motley to William Henry Seward.)
When you click on the ID number of the letter — for example, the letter from James Henderson to Abraham Lincoln — you’ll get a set of vital statistics about the letter (to/from, date, location, number of pages, etc.) as well as a set of images of the reader. The ones I looked at I could not read thanks to both handwriting and fading.
Some of the letters DO have transcripts, also with occasional notes about the letters and content.