Good post Alex! I have been wondering the same thing as well.
On the later cars front spoilers/slpitters are easy, but maintaining the early look and stuff is tough.
Look at the Porsche 911/930 Slantnose. It has louvers above the tire on the wheel well and some other odd things like that. Granted I would not louver my early fenders.
The curvy nature of the Beetle pluss the flat windshield really play hell with its aerodynamics. Just like the 911.
I have seen people weld in weights below the spare tire to keep the front down at speed... I hate to add weight, but it is effective. Also the battery relocation is good as well of cource... Granted then the spare tire needs a new home! So it is a no win there.
After all this ramble I still do not have any good ideas on the matter though