If I can add my two cents in the discussion, I noticed adding jar files inside the nsf will slow down compilation a lot.
What I did is add the jar files as external jar in the Java Build Path.
The bad part is you have to add the jars on every developpers machine file system AND on the server file system too....
But after that the compilation speed was back as it was before.
To add as external jar, first put all your jar files in the notes\jvm\lib\ext of your notes client and in the domino\jvm\lib\ext. of the servers. You probably have to restart the client and the server (I don't remember it was necessary or not).
Then in the designer,
1.open the package explorer,
2. find you DB in the list then rightclick on it
3.Choose Build Path->Configure Build Path in the context menu
4. Go into the library Tab
5. Click on "add external Jars"
6. Select all the jars files you need in your jvm\lib\ext and click the "Open" button
7. Click the OK button to validate your changes in the Build Path
And it should now build your apps with the same speed as it was before.
At least it worked for me, so I hope it will be the same for you !
Hope this helps