Edo Tensei needs the DNA of the person to be reincarnated. (Chapter 520)
Kabuto could not bring back the Uchiha clan because he could not get their DNA.
Danzo, who commissioned the Uchiha clan massacre, must have had their bodies thoroughly destroyed to prevent enemies from misusing the Sharingan. Given Danzo's character and principles, we can be certain he would take such measures. For instance, he was very upset on knowing that Kirigakure's Ao had taken Konoha's Byakugan.
Kakashi also makes a mention of this rule in Chapter 16.
Madara's death was independent of the Uchiha Clan massacre, and Konoha thought he was dead anyway, so the possibility of Danzo destroying his body does not arise at all.
After Madara's death, Tobi must have taken great efforts to make his body inaccessible, because otherwise it would ruin the plan of him falsely assuming Madara's identity. However, he probably did not destroy it completely, and Kabuto (or Orochimaru) may have found the body or its parts somehow. Tobi was understandably shocked when Kabuto showed him the Edo Tensei Madara in the sixth coffin, since it meant his plan was ruined.
Itachi's dead body was easier to obtain, since he died just a few weeks before in his own hideout.