1. General: "HVAC Integration Of The Building Envelope" is a introductory article focused on design considerations regarding the relationship between HVAC components and the roof system. It's a well-sourced article with many useful links for further reading. Available on the Whole Building Design Guide website.
2. General: "Heating, Ventilating, and Cooling Historic Buildings - Problems and Recommended Approaches" is a great article and also worth reading as a general introduction to HVAC systems. The article is from 1991 and available on the US National Park Service's Technical Preservation Services website.
3. Codes: "Duct Insulation and Sealing Requirements in Commercial Buildings" (from 2012) is a handy bulletin available on the US Department of Energy's Building Energy Codes Program website. Includes exterior duct-work. Always verify which building code/energy code is in effect in your area.
4. Rooftop Equipment Screens: See here.
5. Technical: "Guidelines for Roof Mounted Outdoor Air-Conditioner Installations" is available on the website of the Air-Conditioning, Heating, and Refrigeration Institute.
6. Technical: "Attachment of Rooftop Equipment in High-Wind Regions" is an informative little introductory article available at the FEMA website.