CGIwithRで十分なような気もするが、こういったものも試す必要があるかな？WEBアプリだとSOAPでいいんでないとか思うが。

Rserve - TCP/IP interface to R - RoSuDa - Lehrstuhl f

Rserve is a TCP/IP server which allows other programs to use facilities of R (see www.r-project.org) from various languages without the need to initialize R or link against R library. Every connection has a separate workspace and working directory. Client-side implementations are available for popular languages such as C/C++ and Java. Rserve supports remote connection, authentication and file transfer. Typical use is to integrate R backend for computation of statstical models, plots etc. in other applications.