The Replica Program is what gives Vexen use to the Organization, he had been working on, shocker, replicas. Presumably the first product of this program was Xion, an imperfect replica of Roxas created from Sora’s leaked memories of Kairi. Things went awry with her because she began to develop a sense of identity and free will, breaking free of the role of merely a puppet. 

In the manga, Vexen had also created numerous replicas of himself in the event that something had happened to him. These seemed more successful, but most likely due to the fact that they had known they were replicas and knew their purpose. 

Now, I think his greatest achievement was Replica Riku. Why? Because, before this point he had only been replicating nobodies, beings of nothingness that lacked hearts, and thus, were incomplete. With Repliku, he created a full person, but the heart is an unpredictable thing so of course this replica went awry as well with his sense of free will. But that’s the thing, he had a heart.

I like to believe that that was the goal of the Replica Program, to successfully replicate hearts in order to A) simply give them to the Organization members, or B) use them to accelerate the growth of Xemnas’ Kingdom Hearts.