I had the same problem when I updated my Android SDK. Suddenly new projects could not generate the R.java file.
- importing my R.java didn't help because it wasn't generated
- cleaning and building the project didn't help either -- the /gen folder was still empty.
I found that after the upgrade, the adb server didn't start up properly. So a manually started it:
$ cd $ANDROID_SDK/platform-tools
$ adb start-server
Then I restarted Eclipse and did a clean/build on the project, which generated the R.java file.