Many posters believe that the BBC has damaged its credibility as a news organisation by its handling of the affair.
Dr Kelly was named as the key source for a BBC news story about a UK government dossier of information on Iraq's weapons of mass destruction.
On 29 May, Today reporter Andrew Gilligan filed a report in which he claimed that the government had 'sexed up' the dossier. The source for the story was quoted as a 'senior British official'. As a row broke out between the government and the BBC, the broadcaster came under increased pressure to name its source.
Dr Kelly was later summoned by a foreign affairs select committee and faced some aggressive questioning during the hearing. His body was found by police in woodland near his home on 18 July.
Members of the Today message boards have been asking some tough questions of the BBC's reporting standards.
'Ian Doucet' posted a 500-word message entitled 'Questions unanswered by the BBC' demanding answers to a series of points relating to the handling of the affair.
"Gilligan’s report on 29 May was said at the time to be based on a single uncorroborated source, which we now know to be Dr Kelly. But Richard Sambrook, head of BBC News, said on 20 July that Gilligan’s 29 May report was based on several sources of which Kelly was the primary source. Which version is correct?" asks Mr Doucet.
'Art Lines' felt that the BBC's problem was doggedly sticking by the story - and its reporter. "By sticking with the story against all government efforts to get it to prove it, the BBC has put its reputation on the line," he writes.
"After all is revealed, will anyone be able to trust a BBC news item again?"
Another poster, 'Wilf' says: "The days of good old fashioned hard facts have disappeared in BBC reporting. I certainly think the head of news should resign - the fault is his along with the reporter who should also go. The name of the BBC has been besmirched by the attempts to justify its position.
"That's not good journalism; that's just PR self-interest."
One poster defended the BBC's position, stating that the government were wrong to demand that it should reveal its source.
"It has been a tradition of long standing that sources are not revealed, as a way to preserve the freedom of this country," he writes.
A BBC spokesperson told dotJournalism that the message boards were established in 1998 to give licence fee payers the chance to talk to one another and to the BBC.
"They are an important part of our public service role, providing a forum for debate and the opportunity for our users to voice their opinions: the online equivalent of a radio phone-in," he said.
The boards are carefully moderated by the BBC though, and because of the resources needed to monitor them, they are also closed at night.
Free daily newsletter
- Call for Views: UK media invited to shape code of practice on data protection in journalism
- Newsrewired March 2019: seven main takeaways
- BBC Local News Partnerships: how breaking out of the London bubble can strengthen the news agenda
- Local Democracy Reporters supply 850 regional titles with public interest stories
- The Cairncross Report: first impressions