Prosecutors say the men were involved in reconnaissance and planning for a plot with the July 7 bombers who also injured more than 900 others commuters in the co-ordinated morning rush-hour attacks.
Shakil, Saleem and Ali, who all had beards and were dressed in white clothing, waved to friends and family in the public gallery of Westminster Magistrates Court as they were led in for an hour-long hearing.
In custody
The three men spoke only to confirm their names and date of births before being remanded in custody to appear at London's Old Bailey central criminal court on April 20. No formal plea is entered at this stage in British legal proceedings.
Peter Clarke, head of London police's Counter Terrorism Command, said earlier this week that more arrests were likely in connection with the 2005 bombings.
"We now have enough of the pieces in the right place for us to be able to see a picture that is far from complete," he said.
"The search is not over. I firmly believe that there are other people who have knowledge of what lay behind the attacks of July 2005."