Good candidates for Open Source applications are specialized applications that are very costly and cumbersome to develop in general. The availability of the source code makes easy to build programs that take advantage of the work of others. In this sense the Open Source philosophy works in a similar fashion to a free academic exchange. Because of this, Linux has become popular in R&D institutions around the world, and already the Linux applications are too many to count or classify. Among the most propagated uses are:

Clusters for supercomputers with high availability requirements.
Astronomy.
Navigation and subsystems control for satelites and interplanetary exploratory probes.
Computational Network Grids.
Investigations in the field of Artificial Inteligent, Computer Science, Biology,etc...