The dropins folder supports a variety of layouts, depending on the scale of your application and the desired degree of separation of its parts. The simplest layout is to just drop plug-ins in either jar or directory format directly into the dropins folder:
eclipse/ dropins/ org.eclipse.core.tools_188.8.131.52710121455.jar org.eclipse.releng.tools_3.3.0.v20070412/ plugin.xml tools.jar ... etc ... ...
You can also drop in the traditional Eclipse application or extension layout directly in the dropins folder:
eclipse/ dropins/ eclipse/ features/ plugins/
If you have various different components being dropped in, and you want to keep them separate, you can add an additional layer of folders immediately below the dropins folder that contain traditional Eclipse extensions:
eclipse/ dropins/ emf/ eclipse/ features/ plugins/ gef/ eclipse/ features/ plugins/ ... etc ...
Finally, you can add link files as in the traditional Eclipse links folder:
eclipse/ dropins/ emf.link