A parade to mark the departure of the squadrons from RAF Lyneham took place at the Wiltshire air base on Tuesday.
RAF Lyneham is due to close at the end of 2012 with the majority of its planes, kit and personnel moving to RAF Brize Norton, in Oxfordshire.
Repatriations of fallen troops, which have taken place through Lyneham since 2007, will go through Brize Norton from September.
Princess Anne attended the farewell parade, with 100 station personnel.
RAF Lyneham opened in 1939 and the first Hercules transport plane arrived in 1967.
The last Hercules is due to leave the base on 1 July.
The Princess Royal, Lyneham's Honorary Air Commodore, paid tribute to the famous "home of the Hercules".
"My association after 34 years also finishes and I will, I think, miss that rather distinctive sound of a Hercules tracking into Lyneham from the north as they track over Gatcombe," she said.
Station commander, Gp Capt John Gladstone, said the base had been central to Britain's defence force.
"We've supported a whole string of campaigns over the decades whether it was the Falklands conflict or the two Gulf wars, the Balkans episode or whether it was areas like Sierra Leone, Afghanistan or Iraq.
"It's been, I suppose, the base plate from which a lot of UK defensive campaigns have been launched."
John Beauchamp from the RAF Lyneham Old Boys' Association worked on the first Hercules to arrive at the base.
He said it was a "very emotional day".
"I saw this building built," he said.
"And I was watching those lads and lasses on parade and you could see it in their faces as well - there's a lot of sadness today."