Clark's research work concerned geometry pipelines, specialized software or hardware that accelerates the display of three dimensional images. The zenith of his group's advancements was the Geometry Engine, an early technology for rendering highly graphical computer images he developed in 1979 with his students at Stanford.
In 1982, Jim Clark and Abbey Silverstone along with several Stanford graduate students formed Silicon Graphics, Inc. The earliest Silicon Graphics graphical workstations were mainly terminals, but soon newer models were stand-alone graphical UNIX workstations with very fast graphics rendering hardware.
During the mid-1980s, Silicon Graphics began to use the MIPS CPU as the foundation of their newest workstations, replacing the Motorola 68000. Soon, Silicon Graphics became the world leader in the production of Hollywood movie visual effects and 3-D imaging. Silicon Graphics did not rely on high sales as they could charge more for their special high-end hardware and special graphics software.
However, by the early 1990s, Clark had a falling out with Silicon Graphics management and got the itch to start a completely new and different enterprise. In 1994, Clark and Marc Andreessen, the co-creator of the World Wide Web browser Mosaic, founded Netscape. The founding of Netscape was a pivotal point that helped launch the Internet IPO boom on Wall Street during the mid to late 1990s, and Clark reaped the financial benefits of the Internet boom -- with an investment of $5 million US, he earned $2 billion US. Just as the Internet boom was about to completely bust, Clark got the urge to move on again.
In 1998, Jim Clark came up with the idea of streamlining the insurance hassles and paperwork associated with the healthcare industry. He came up with the idea of a company that would help make access to more efficient healthcare easier. Although his original idea was a bit too ambitious, it did lead some inroads in administrative streamlining of medical records technology, but an Atlanta, Georgia startup company, WebMD, was already making inroads toward the same goal. Knowing that WebMD had financial backing from Microsoft, Clark decided to merge his newest startup, Healtheon, with the original WebMD to form the current WebMD Corporation. WebMD also provides a vast resource of online, reliable health information on the Internet.
In 1999, Jim Clark launched myCFO - a company formed to help wealthy Silicon Valley individuals manage their fortunes. While Jim Clark served on the Board of Directors most of myCFO's operations were sold to Harris Bank in late 2002 and now the successor operates as Harris myCFO or Harris/myCFO.
Clark was a director and investor in biotechnology company DNA Sciences, founded in 1998, which went bankrupt and was acquired by Genaissance Pharmaceuticals Inc. in 2003.
In 1999, Clark donated $150 million to Stanford University for the creation of an interdisciplinary biological sciences program called Bio-X. In October 2003, the James H. Clark Center for Bio-X was completed largely in part to his funding.
In the Fall of 2005 Clark and David Filo of Yahoo! each donated $30 million to Tulane University's School of Engineering for merit based scholarships to provide education to deserving students regardless of financial situation in the discipline of engineering. However, after Tulane's restructuring that saw the elimination of nearly all engineering disciplines, the board requested Clark and Filo allow the funds to be used for other programs.