The monarch spoke of her sadness at the heavy death toll suffered by fighting the Taliban factions and she praised the stoicism showed by bereaved families of servicemen killed on operations.
She said Britain owed a profound "debt of gratitude" to all past and present troops who have served in the Afghanistan conflict.
She said: "I am sure that we have all been affected by events in Afghanistan and saddened by the casualties suffered by our forces serving there. Our thoughts go out to their relations and friends who have shown immense dignity in the face of great personal loss.
"We can be proud of the positive contribution that our servicemen and women are making, in conjunction with our allies. Well over 13,000 soldiers from the United Kingdom, and across the Commonwealth – Canada, Australia, New Zealand and Singapore – are currently serving in Afghanistan. The debt of gratitude owed to these young men and women, and to their predecessors, is indeed profound."
The number of British military personnel who have died in Afghanistan so far this year now stands at 106 – with four deaths coming in the past six days – the highest annual tally since the 1982 Falklands campaign.
Echoing her 1992 Guildhall speech, when she labelled the year an "annus horribilis", the monarch this time described how some years are "best forgotten".
"Each year that passes seems to have its own character. Some leave us with a feeling of satisfaction, others are best forgotten. 2009 was a difficult year for many, in particular those facing the continuing effects of the economic downturn."
She delivered her speech from Buckingham Palace's White Drawing Room, standing in front of a decorated Christmas tree with a small collection of family photographs nearby. The Christmas message is the sovereign's opportunity to address the country directly and it is written without the help of aides or advisors.
It also featured praise for the Commonwealth – an institution which celebrates its 60th anniversary this year. The Queen said the family of nations "remains a strong and practical force for good" and that it was an opportunity for its people "to work together to achieve solutions to problems".
She urged the institution, especially its youth, to continue discussions about important things such as the environment.
As a counterpoint to the Queen's message, the model Katie Piper was enlisted to deliver an alternative speech, following in the footsteps of Doreen Lawrence, Marge Simpson, Jamie Oliver, Ali G and Mahmoud Ahmadinejad.
Ms Piper, delivered a message of hope and spoke of the emotional effect of being disfigured in a violent assault.
In March 2008, she was scarred in an acid attack organised by a man she had met on the social networking site, Facebook. A cup of industrial strength sulphuric acid was thrown at her in the street by his accomplice.
It left her blind in one eye, with thirddegree burns and internal damage.
"I made a choice that the men who did this to me wouldn't destroy me," she said. "I was forced into a situation where I had to be strong. The human body is amazing in how it can repair itself, but it's a mental struggle in the end."
Daniel Lynch, who raped her then organised the attack, is now serving two life sentences. Stefan Sylvestre, who threw the acid, is also serving a life sentence.
She now continues to model and refuses to let her disfigurement limit her life. "And why shouldn't I model like I used to? I'd like to model clothes with my scars showing. That's how you start to change perceptions of what beauty is," she added.
Meanwhile, Britain's church figureheads raised concerns over Britain's young and the pressures upon them.
Rowan Williams, the Archbishop of Canterbury, suggested that children were forced to grow up too quickly in his Christmas sermon.
Preaching at Canterbury Cathedral, Dr Williams criticised the rush to create independent citizens who could stand on their own two feet, and said that being "dependent" on parents did not have to be seen in a bad light. He urged parents to treasure the dependency of their children. Rushing them to become independent was only leading to misery and exploitation, he added.
Dr Williams also highlighted the plight of hundreds of thousands of children who were being exploited in "civil wars in places like the Congo and Sri Lanka – children who are abducted, brutalised, turned into killers, used as sex slaves ... their suffering is an insult to the purpose of God, a contemptuous refusal of the gift of God on the part of those who keep them in their different kinds of slavery," he said.
The Most Rev Vincent Nichols, the leader of Catholics in England and Wales, also drew on the experiences of many young people who had been drawn into gang membership in an attempt to bolster a sense of identity, in his first Christmas Midnight Mass as Archbishop of Westminster.
He spoke of the longing for a sense of community and said a visit to Feltham young offenders' institution in west London reminded him of "so many" young people who have resorted to gang violence.
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