A lot of that depends on the distro you're using and whether you're installing these resources as OS packages or manually. Unlike most system components, I prefer manual installation of Tomcat.
The Red Hat rpm installs the JDK under /usr/java/xxxxx, where "xxxx" is a name that indicates the JDK version, so all your different JDK's and JRE's can live in the same place. I normally unzip Tomcat into the /usr/local directory, although strictly speaking, this isn't ideal behavior anymore. I also create a tomcat user and group ID so that Tomcat doesn't have to run as root.
An IDE is no substitute for an Intelligent Developer.
Joined: Jan 31, 2010
May compile java apps like chat or bit torrent on virtual dedicated server Linux?
After use JRE to run them, if prefer for ever to be running?