The following archives holding Me 163 material have been identified:
Deutsches Museum, Munich. See the drawings page (on this site) for a listing of the folders in the archive.
Dasa, a.k.a. DaimlerChrysler Aerospace, formerly Daimler-Benz Aerospace. Dasa has an archives section at its main offices at Ottobrun, holding Messerschmitt, Bölkow and Blohm documents
Bundesarchiv - Abteiling Militärarchiv in Freiburg holds many military documents that must include Komet material. I've read that searching this archive is not easy however.
Imperial War Museum. A first inspection of the Duxford library turned up some Komet material. The MINTEC microfilm archive (a partial copy of the NASM archives) included some some structural dimension data. Another document found here was 'CIOS XXXII - 37: Messerschmitt Aircraft Design'. The 5,000,000 photograph collection is also likely to contain some Komet material.
The National Archives (formerly Public Records Office), London. Since late 1999, the PRO has an online search engine, which makes researching a lot easier. They hold at least some interesting documents on the Messerschmitt 163 and the Walter rocket engine.
Keele University has all existing RAF aerial reconnaissance photos from WW2 in its 'Air Photo Archive'. This collection should include Komet bases like Peenemunde, Bad Zwischenahn, Venlo, Brandis and Jesau.
National Air and Space Museum, Washington DC. There are a total of 457 Me 163 documents on microfilm reels, of which 34 are manuals. Also listed are a general parts list, consisting of 54 pages of tables (reel 2832, frame 1204) and a short Ersatzteil-Liste (replacement parts) consisting of 53 pages of tables and diagrams or drawings (reel 2499, frame 464). The collection is slowly digitized, and Bernard Biales and Ronnie Olsthoorn found the following Komet-related online documents so far:
Captured German Aeronautical Documents (CGD) Microfilm - CGD-28: Me 163B Airplane Manual, Part 6 - Power Plant - Description, Part 7 - Power Plant Control and Maintenance, English translation, 27 pages. I don't know why this document separately lists these chapters, since they are also included in the full translation in CGD-256.
Captured German Aeronautical Documents (CGD) Microfilm - CGD-234: Theories About Tailless Airplanes, English translation of 'Theorien am schwanzlosen Flugzeug', 10 pages
Captured German Aeronautical Documents (CGD) Microfilm - CGD-245: Description of the Me 163B-0 Construction, English translation, 48 pages. Includes some performance figures. The source document is 'Baubeschreibung Me 163 B-0' but I have never seen that document.
Captured German Aeronautical Documents (CGD) Microfilm - CGD-255 : Me 163, Volume I - Service Manual and Spare Parts List, English translation, 180 pages. I think it is a compilation of two German documents. The first source document is 'Me 163B Bedienungsvorschrift-Fl, L.Dv. T.2163B/Fl.' but an earlier version compared to mine that includes engine maintenance procedures. The second source document (page 75) is some kind of spare parts list.
Captured German Aeronautical Documents (CGD) Microfilm - CGD-256: Me 163, Volume II - Me 163B Airplane Manual, English translation of 'Me 163B Flugzeug-Handbuch, D.(Luft)T.2163B', 596 pages (297 actually thanks to nearly 300 blank pages). Compared to my German paper copy from Luftfahrt Archiv Hafner, this translation is more complete: it includes chapter 8A2 for the MK 108 (page 383), chapter 9C1 for the hydraulic system (page 477), chapter 9D for the radio (page 513), chapter 9G for equipment and special tools (page 535), and chapter 10 for transportation and salvage (page 557). On the other hand, many chapters in this translation are older than in my paper copy. For example the translation of chapters 4, 6, 7 and 9B1 are from August 1943, my German-language copy shows June 1944. The photos in the translation are usually of very low quality.
Iowa State University, Ames, Iowa. The ISU Library Special Collections Department holds the 'Alexander M. Lippisch Papers' that includes a lot of material that Dr. Alexander Lippisch took with him to the USA. The compiled a 113 pages listing, that mentions 100 boxes, 9 tubes, 6 mapcase drawers, 7 lantern slide boxes and 12 boxes of film. This most likely covers all of Lippisch' work, so only a part covers the Me 163. Identified were quite a few files on the Me 163 and its variants and testing.
Planes of Fame museum is said to have been given a complete set of Komet drawings by the NASM. The story goes it was one of two sets found on the German submarine on its way to Japan. The museum curator however cannot locate the set.
The Canada Aviation Museum has an on-line digital archive, that includes a fair number of Komet photos, mostly made during the restoration of the museum's Komets