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You will need an SAP OSS ID and password to download JCo from http://service.sap.com/connectors. At this site, you will find version for both Windows and Linux. The Java development on each platform is similar, but you will need to ensure that the Java Native Interface libraries can be found in your system path.
Using Tomcat (an open source Java app server) you can deploy Java servlets and JSPs that use the JCo libraries to make RFC and BAPI calls. This outside-in approach allows you to access SAP functionality outside of the system. You can also use JCo from within SAP to call external Java libraries. This does not require Tomcat, per se, unless you are developing high traffic Java applications that need to deal with a lot of traffic from SAP. In that case, you would likely encapsulate your Java functionality in Enterprise JavaBeans, to better manage traffic loads.
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