All five families threw flowers on top of the hearses, with some mourners touching the glass and hearses as they wept.
Five minutes later, the coffins, draped with Union flags, were then driven to the John Radcliffe Hospital in Oxford.
The crowds loudly applauded as the hearses drew away to the peal of bells.
Following the deaths of the five men, the Ministry of Defence and their families issued touching tributes.
Group Captain Richard Maddison, Station Commander at RAF Odiham, where all of the five men except L/Cpl Thomas were based, said: "As with all losses of personnel in Afghanistan, we mourn the loss of our most capable and dedicated personnel, who served without complaint and in full understanding of the risks associated with their roles.
"They were fine ambassadors for their unit and for defence as a whole, and we shall not forget them."
Capt Clarke, 30, from Cowbridge, South Wales, was a pilot and "rising star" in the AAC who was "full of life and immensely committed to his soldiers and friends".
WO Faulkner, 38, was an "experienced aviator, loving husband and hugely dedicated father to two children" who had been deployed to Afghanistan on numerous occasions.
Cpl Walters, 36, known as Bungle, was a "highly respected" junior non-commissioned officer who had deployed to Afghanistan on numerous occasions.
Regularly at the centre of any debate, especially when the subject involved rugby or Cornwall, the helicopter's gunner was known to be a "consummate professional".
Flt Lt Chauhan, 29, from Birmingham, was on his third tour of duty in Afghanistan as an intelligence officer when he died.
Known as Rak to his comrades, he was said to be "charming, funny and sharp as a tack".
L/Cpl Thomas, 26, from Brecon in Powys, Mid Wales, had volunteered for deployment to Afghanistan and arrived there in December last year.
His family described him as a "truly amazing person, living his life to the full, while fulfilling some of his many dreams and adventures".
The helicopter in which the men were travelling is believed to have been from AAC 657 Squadron, a top unit based at RAF Odiham which provides support and transport for special forces troops.
The aircraft went down in the Takhta Pul district of Kandahar, in what was the worst incident involving a British military helicopter in Afghanistan since the war began there in 2001.
The crash caused the third biggest single loss of life of British troops since the conflict in Afghanistan began and brought the total number of service personnel killed there to 453.
The incident equalled the previous worst disaster involving a British helicopter, when a Lynx aircraft crashed in Basra City, Iraq, in May 2006 killing the five service personnel on board.
Speaking after the moving service, Lynn Little, mayor of Carterton, described the large turnout as "tremendous".
Councillor Little, who also acts as a liaison officer for the bereaved families, said: "It was a very sad occasion but then it always is.
"We are proud of our service families and serving personnel, when something tragic like this happens the least we can do is support them on a day like today.
"There are a tremendous amount of people here today, there are around 300 Army Air Corps and then a lot of local people too.
"As mayor, I am very proud so many have come out to offer their support.
"It is something we don't want, we wish it didn't happen but when it does we get out here for these families."
