Feversham College, Bradford, tops the "value added" measure - which overall sees grammar schools doing very well.
Value added shows how children's attainment rose between their final primary school year and their GCSE year, rather than just the end results.
We also heard from Stephen Twigg, the School Standards Minister
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But the performance tables have still been criticised by unions, opposition politicians and independent schools.
Feversham College, which was in the independent sector until 2001, scored 1,099.8 on the new "all through" value added measure, which is based around 1,000.
LEAGUE TABLE FACTS
Best for adding value: Feversham College, Bradford
Grammar schools outperform comprehensives
Best GCSE score: Thomas Telford CTC
Best A-level score: Colyton Grammar School
53.7% got five or more top grades at GCSE-level
57.4% in specialist schools compared to 48.2% in others
London fastest improving region
The school said it was underpinned by its Islamic ethos.
"Our added value has increased because we monitor student progress and teaching and learning with a rigorous focus on exam preparation."
Nationally, though, teenagers in comprehensive schools averaged a score of 984.
In grammar schools the figure was 1,021. In secondary moderns, 982.9 - just below the comprehensives.
The chair of the National Grammar Schools Association, Brian Wills-Pope, said: "What this shows is that selective schools do get the best from their students and it goes to prove that we do add significant value."
The average in community special schools, which do not normally feature in the tables published by news organisations, was 1,013.2.
In independent schools - selective and non-selective - the average was 1,034.2, though they choose whether or not to have their individual scores published.
In the main GCSE-level tables, students at Thomas Telford city technology college (CTC) in Shropshire did best by far.
All its 15-year-olds get the equivalent of 12 good GCSEs, averaging 760.3 points - much more than any other school, including grammars and independents.
This year's tables count a much wider range of vocational qualifications at this level.
The Independent Schools' Council, drawing attention to such things as cake decorating certificates, said they had become "absurd".
At advanced level, the students at Colyton Grammar School in Devon took top slot by averaging 512.6 points.
An inner-city comprehensive which has had an increasingly "can do" attitude in recent times heads this year's "most improved" list.
The proportion getting top GCSE-level grades at Sir John Cass Foundation and Redcoat Church of England Secondary School in east London has gone up by 51 percentage points since 2001, to 87%.
This is the third year the school has topped the list - but it shares the honour this time with The North School in Ashford, Kent.
Its performance has also risen 51, from 9% to 60%.
The School Standards Minister, Stephen Twigg, who visited another of the most-improved schools, said: "These figures show that the fastest improvement is being made in areas of significant deprivation and historically low achievement."
The Liberal Democrats said it was time to abandon the "meaningless" tables - which hid the fact that two thirds of students still failed to gain the national standard in the core curriculum subjects of English, maths and science.
The leader of the Secondary Heads Association, John Dunford, said: "Although more difficult to interpret, the greater complexity of this year's tables is welcome in avoiding the simplistic approach of previous years and giving parents a broader view of the achievements of schools."
But the tables were "deeply flawed", and created perverse incentives for schools to change their exam policy and even curriculum to improve their standings.