In Eclipse prior to 3.4 you could have a number of external "Extension Locations" for plugins/features you didn't want in the Eclipse installation directory or that you wanted to share among multiple Eclipse installations. In the Update Manager wizard you could have even selected that you want a plugin installed into a particular extension location. Since Eclipse 3.4 (Ganymede) this isn't possible anymore.
Problem 1: Links to the external Extension Locations are ignored
Prior to 3.4 you could have directories with plugins and features (extension locations) outside of the Eclipse installation directory ($ECLIPSE_HOME). To let Eclipse know about them you created a file in the directory $ECLIPSE_HOME/links/ containing the text path=/path/to/your/extension/location. Unfortunately Eclipse 3.4 ignores these links. But nothing is lost - move them into the new directory $ECLIPSE_HOME/dropins/ .
Actually you don't need to have only link files in the dropins directory, you can have there individual packed (.jar) or unpacked plugins or complete extension locations (eclipse/...) either directly under dropins/ or in some subdirectory, e.g. dropins/jboss-tools/eclipse/... .
Problem 2: The new update manager doesn't let me select where to install plugins
The new plugins management (also known as provisioning system) installation wizard doesn't let you select where to install the downloaded plugins. It should support something called Bundle pools, that is shared plugin installation folders that can be used by multiple installations of Eclipse but the current user interface doesn't provide any such options and it also may not be exactly what you need.
If you don't want to simly forget about installing plugins outside of Eclipse itself, there is a solution - you may re-enable the old Update Manager and proceed as you're used to. To enable the Update Manager go to Window > Preferences > General > Capablilities and check Classic Update. If you don't see the option Capabilities (e.g. if you've the Java EE Eclipse package) then you can:
1. Either Open the Help window and search for “Manage configuration”, then select ” Enabling, disabling, and uninstalling features”. The help window gives a link to “Help > Software Updates > Manage Configuration.” (by Ronan);
2. Or install Eclipse SDK and restart Eclipse.
Mum, why did all this happen?
All this happened because the old plugin management stuff was replaced by a more clever and capable new provisioning system Equinox/p2. I'd recommend you to read its Getting Started guide. You can learn there about the new directories dropins/ and p2/, about Bundle Pooling (sharing of plugins among Eclipses) and other features.