I've had troubles where re-running the application would launch a new instance instead of re-using an existing, open emulator. The way I've solved this is to have it ask me every time which prevents new ones from launching.
To allow Eclipse to prompt you:
- Open the Run menu > Run configurations
- Within the new window, double click Android Application
- This creates a new run configuration
- Open the Target tab
- Select Always prompt to pick device
- Click Apply
- Click Close
Launch a new emulator the first time and leave it open.
Now the next time you run your application, it will ask you to start a new emulator or use one that is already open. Choose the one that is already open.
This also has the added benefit of allowing you to choose different AVD versions to test your app if you have multiple versions of emulators with different versions of Android.
Also you are able to plug in your phone to your computer via USB and it will appear in this list as well.
I've found this to speed up testing dramatically for me.