After upgrading to Mavericks I noticed that Java was no longer present on my system. Java-based applications such as PyCharm would no longer run and browser-based applets would display a plugin missing error in both Safari and Chrome. To get up and running again, two installs needed to happen.
First was the runtime. You can download Java for OS X 2013-005 directly or the OS will automatically download and install it if you launch a Java-based application such as PyCharm.
Once installed, $ java -version returns 1.6.0_65:
The second step was to install Java 7 from Oracle. Unfortunately this version of Java is only compatible with 64-bit browsers such as Safari. To use Chrome (still 32-bit), you must then disable Java 7 and re-enable the Apple-provided Java SE 6 web plug-in by following these simple steps.