Waterjet machines are not specialty machines for niche applications. They are general purpose tools that are useful in any machine shop. Following is is a small sampling of specialized applications.
General purpose machine shops
Waterjets are good all-around machine tools, as it is fast and easy to go from idea to finished part. Waterjets can also work with many different types of materials with minimal fixturing and setup.
Artists
Artists use waterjets because they can create intricate designs in materials that have traditionally been difficult to work with, such as stained glass, marble and stone.
Architectural
Similar to the art market, there are many machines out there making custom flooring from stone, as well as making architectural details from metal.
Aerospace
Companies that makes parts for the aerospace industry maching lots of aluminum, which is easily machined on a waterjet. Exotic metals such as Inconel®, titanium, and Hastalloy can also be machined by waterjets.
Manufacturing
Waterjets are used for making parts of products that are sold, as well as many of the parts used to make the machines on the assembly lines.
Automotive & transportation
Prototyping and production parts for automobiles, and the tooling for making automobiles. Also there are a lot of custom race car parts made on waterjets.
Laser shops
Lasers and waterjets are highly complementary tools. They both pick up where the other leaves off.
EDM shops
Some of the small size and higher precision waterjet machining centers are great complementary tools to EDM because they allow for higher speed machining of similar shapes, and can provide other services for the EDM such as pre-drilling start holes or stress relieving the part prior to skim cutting on the EDM.
Model shops / rapid prototyping
Fast turn-around of single piece production in nearly any material makes waterjets great for these kinds of applications.
Schools
Many of the larger size universities that offer engineering classes also have waterjets. They are great tools for the classroom environment because they are easy to learn, program, and operate, and because they can make one-off kind of parts quickly. They also provide a great service to other departments within the university that may need job-shop services.