A lack of services for children with special educational needs topped school-related complaints, in a breakdown of the assistance provided by the children's commissioner's office over 12 months.
Other cases taken up by the office ranged from bullying and alleged abuse by teachers and headteachers.
One primary school pupil wrote to the commissioner asking for his help in stopping her teacher bullying her. In another case, an 11-year-old upset at being parted from her friend at secondary school was offered a place at the same school after the commissioner's intervention.
Teachers and governors were also regular callers to the commissioner's office in 2004-05 - often to seek advice on how to deal with allegations of abuse and child protection. Mr Clarke's third annual report, published this week, focused on respect. He claimed adults still did not show children enough of it, and that Prime Minister Tony Blair's "Respect" campaign, targeting anti-social behaviour, had made things worse.
In 2004-05 the commissioner's office dealt with 279 more cases than the year before, with 41 per cent relating to men or boys, 34 per cent relating to females, and 25 per cent concerning mixed-gender groups.
But parents were more likely to make initial contact with the office than children, accounting for just over half of cases. The largest age group seeking help was teenagers aged 14 or 15.
Protection issues, particularly internet safety, and the treatment of looked-after children by social services, also featured in the commissioner's report.
Mr Clarke called for teachers to be trained in internet use and abuse.
While pupils far outstrip adults' technical abilities on the web, they still need guidance on how to use the internet and new technologies safely, he said.
Teacher-training colleges should also ensure all newly-qualified teachers are trained in the safe use of the internet to stop rising cases of internet abuse - including "grooming" by paedophiles and bullying.
Elsewhere, Mr Clarke attacked the Assembly government's attempts to tackle child poverty in Wales, the headline issue in Mr Clarke's first annual report in 2002.
A fair future for our children, an Assembly government policy strategy, was published in February last year as a result. However, Mr Clarke said he had been concerned by a "lack of urgency" in drawing up an action plan that could take up to a year to complete. In his first report, Mr Clarke attacked child poverty in Wales as a "national disgrace".
Mr Clarke is also to consult the Assembly government over a lack of school nurses.
Latest figures from the Royal College of Nursing reveal some school nurses in Wales are responsible for more than 6,000 pupils.
Mr Clarke said his priorities for 2006-07 included launching a dedicated freephone helpline for children and young people, and tackling bullying.