The blasts in February and August 2004 left 50 people dead and more than 150 wounded.
The three men were convicted of terrorism, murder, and banditry, among other charges.
Prosecutors said two of the men, Maksim Panaryin and Tamby Khubiyev, belonged to a terrorist group based in the Karachayevo-Cherkessia Republic, in Russia's North Caucasus.
The third man, Murat Shavayev, is reportedly a former Russian Justice Ministry official.
Prosecutors and lawyers of the victims said they were satisfied with the verdict.