General Web Programming Trends

Servlets

Very fast compared to CGI's (quoted as 6 times higher throughput) as a web request invokes a new thread instead of a new process
Session management comes for free with Servlets
Being in Java, servlets are very easy to develop as

memory leaks are eliminated
Java talks very well to C
Java talks very well to Oracle or any SQL-compliant database via JDBC (which depending on the implementation can be made platform independent)
there is a huge amount of freeware for developing servlets

e.g. The Espresso framework from http://www.javacorporate.com which is freeware for connecting to dbs via servlets and JDBC
The Element Construction Set (ECS) available from http://java.apache.org
Jyve a FAQ management system using Java Servlets available from http://java.apache.org
Slide, a distributed Authoring and Versioning System (available at http://jakarta.apache.org)
JetSpeed (an Enterprise Information Portal software) (I haven't used this)

JSPs (Tomcat at http://jakarta.apache.org)

Based on Servlets, these allow for tags that invoke servlet functions within HTML pages.

So one could, on a JSP capable server, store a HTML page that contained function calls to Java functions (servlets) in tags within the page.
Before the JSP server, serves this page to a client, it will run the Java functions in the JSP tags, and replace the servlet tags with the output of these functions.

This is enabling the creation of TAG function libraries (called taglibs) which could then be used by web designers. For example, one could provide taglibs that contained functions for validating a SMILES and if correct, then searching a thor database for data on the SMILES. With the right design, these taglibs could be made very powerful and useful.

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