Mac OS / Mac OSX

• bouncing dock alerts: http://www.amug.org/~glguerin/sw/index.html#notifications
• Res Café: Swing-based Java utility for reading and extracting resources such as ICONs and MENUs from the Resource Forks of Macintosh files http://freshmeat.net/projects/rescafe/
• http://www.roydesign.net/mrjadapter/

Windows

• XLNT Java Utils: http://www.xlnt-software.com/: These utilities provide some added functionality to the Java platform. They allow the programmer to create and read symbolic links (shortcut/.lnk files under Windows), read and write registry values (Windows only), launch a file through the IShell API (Windows only) and have a system-tray icon with associated menu options (Windows only).
• Systray for Windows and KDE
• Java System Tray Manager (not to be confused w/ Systray for Windows and KDE)
• Windows Tray Icon - Java Implementation
• JTray - Commercial Windows tray library.
• Simple JNI makes writing JNI code for Win32 very easy.
• JNIWrapper makes writing JNI code for Win32 very easy. Ships with Winpack library. It allows the programmer to (i) open native dialogs (color, file and folder chooser), (ii) create transparent, custom-shaped native windows, (iii) read and write the registry, (iv) access shell funtionality (systray, shell folders, system colors and symbolic links), (v) access system services and (vi) embed OLE components, such as Adobe Reader, Internet Explorer, Flash player and MS Office applications.
• Object-Oriented JNI for DOTNET (low-level) implements pure JNI interface for developing managed code with .NET1.1 and .NET2.0 (without use of any other technologies like COM, SOAP, CORBA, etc.). This API (1) allows to implement Java native methods with DOTNET delegators without P/Invoke, (2) wraps all standard JNI references with simple objects, (3) array classes can handle multidimensional Java arrays, (4) implicitly does all conversions from Java to DOTNET types and vice versa, (5) embeds Java components to DOTNET GUI and .NET components to Java module, (5) implements Java native methods with .NET code like in C++ JNI (loads Assembly Module with System.loadLibrary(...) or System.load(...) ).

• JavaUnix^? http://www.xenonsoft.demon.co.uk/products/javaunix/index.html
• http://escher.sourceforge.net/ X11 Hooks (I'm not exactly sure what this does. I'll need to try it out.)
• http://wiki.java.net/bin/view/Linux/WebHome Linux.Java.Net wiki

Built in to Java

• JAWT: Provides the ability to embed native code in Java that renders on AWT/Swing components
  • http://java.sun.com/j2se/1.3/docs/guide/awt/AWT_Native_Interface.html
  • http://java.sun.com/developer/technicalArticles/Programming/embedjava/

Other

• Java Tip 66: Control browsers from your Java application
• sourceforge BrowserLauncher - a valiant effort to collect ad-hoc rules for launching system browsers via Runtime.exec
• JDIC a java.net project for Java Desktop Integration
  • potentially useful project - but for a "Desktop Integration" project - why is there no Start menu (and GNOME/KDE/CDE) manipulation API?