This year's subject league tables, which appear on the Complete University Guide website, show Cambridge University, Imperial College and the London School of Economics outperforming Oxford.
They also show that universities belonging to the 1994 Group of small and beautiful universities are doing increasingly well and coming ahead of members of the Russell Group.
St Andrews comes fifth, Bath sixth and Durham eighth. This year, the coverage has been expanded to 62 subjects and, like last year, they rely on only four measures: student satisfaction, research assessment, entry standards and graduate prospects.
Paul Marshall, the executive director of the 1994 Group, attributes this success to the small size of these universities but he says that funding is a problem. "Our size allows change to happen faster. In the Russell Group, it is much more of a challenge to make changes.
"The older universities get a lot of funding from alumni and donors but a number of our universities are quite young. The challenge for us is to start generating real funds that give us flexibility and to have less reliance on state funding."
Marshall says that in a decade he would be very disappointed if the 1994 Group universities were not dominating the top 10. But will they ever be in the top two? "That's a longer term goal," he says.
St Andrews has 92 per cent of its subjects in the top 10, well ahead of Edinburgh, which is in 14th place and Leeds, which comes in at 25.
Dr Louise Richardson, the new principal of St Andrews, agrees that the real reason for her university's success is its size.
"We are the ideal size," she says. "We are big enough to compete for the best academics and students but small enough to have an impact on the life of every student who comes here."
She hopes to keep up these standards: "I plan to keep focusing on excellent research and excellent teaching but this will be tough in the economic climate."
Founded in 1892, Durham, one of the older universities in the 1994 Group with 15,000 students, has risen above universities such as Warwick and Bristol in the subject tables.
"Durham has always been right up there", says Professor Christopher Higgins, the university's vice chancellor.
"The only difference is the size of the university. In many areas we are more competitive than Oxford or Cambridge. There are some subjects we teach, which are thought to be the best in the country."
Bath has 77 per cent of its subjects in the top 10. While the university cannot boast the same splendid Georgian architecture as the town, it offers its 13,000 students a university which is rivalling some of the older institutions as well as fantastic sports facilities and a lot of green space.
The pro-vice chancellor,Professor Ian Jamieson, says: "Our academic portfolio is distinctive because of its blend of practical, experience-based learning and research-led intellectual challenge. The benefits of this approach are clear from the excellent career prospects that our graduates enjoy."
The School of Oriental and African Studies (Soas) in London, comes in at No 15. With about 4,400 students, it is the smallest in the subject table.
Professor Paul Webley, the Soas director, says: "Because the 1994 Group universities are smaller they have a strong sense of community. That is attractive for students and staff."
The key is to focus on an area and become good at it, he says.
"Soas has long been an excellent university with a very distinctive focus. I think that universities cannot be all things to all people."
One of the surprises is Harper Adams University College in deepest rural Shropshire, which appears three times in the table and comes top for agriculture and forestry.
Named after a wealthy gentleman farmer, it has been an agricultural college since 1901 and has risen above Cardiff and Leeds, to No 2.Its position shows that specialisation can work.
The college is set in 700 acres of Shropshire countryside and has its own 175-hectare farm where students can practise what they learn.
It offers courses such as veterinary nursing, off road vehicle design and leisure and tourism management.
The college has excellent employment prospects, which is largely down to its business links with companies such as JCB, Marks and Spencer, Tesco and the National Trust.Reuse content