Mask Works
A mask work (or integrated circuit layout) is the set of photolithographic masks for the creation of an integrated circuit chip. These chips are made up of a series of layers, each of which is created using a mask which works something like a stencil. The problem is that the mask designs are not themselves patentable subject matter. Nor can the functional benefits be protected by copyright; copyright protects art, not functional data.
Therefore, a special treaty created a special right to offer copyright-like protection to mask works, which was later integrated into the Trade-Related Aspects of Intellectual Property Rights (TRIPS) agreement.
Software
Computer software has had an uncomfortable relationship to IP. Like mask works, software is generally considered non-patentable as an abstract idea. After all, the software itself is just one or more instructions or algorithms. For a while, software was copyrightable (because it was written down), but that only protected the specific code as written; functionally identical code that was not identical in form was not protected.
Currently, the patentability of software does not have a bright-line rule. Generally, to be patentable, the software must be tied to something concrete or physical. Generally, software “as such” or implementing an abstract idea like a method is not patentable, but software for controlling a physical device may be.
Design Patents
The design patent/industrial design right is a patent for the visual design or features of objects that are not completely utilitarian. It’s interesting because the design patent provides less protection than a copyright; typically 15-25 years instead of the 70+ of a copyright. In addition, other protections may still be available; a design that amounts to trade dress or trademark may be protected by those, as well.
Biologicals
Naturally-occurring substances may not be patented. However, naturally-occurring DNA or substances, if “isolated” from their natural occurring state, or artificially-produced, may generally be patented. This is one of those situations where the purpose of a law - with patents, to incentivize innovation - creates what appears to be a perverse outcome. The benefits of using these substances, including insulin, GMOs such as Golden Rice, and DNA research, are seen as being worth the cost of a state-granted monopoly (though there is significant debate on the ethics).