Yes, they were all programs. Were any of them made for any other intent like the Mero's? I really don't think it's likely. Neo's already carries the anomaly code -- it's part of who he is. It wasn't placed there by some machine programming wizard -- the machines would just delete it and be happy if that were the case.
Architect: Your life is the sum of a remainder of an unbalanced equation inherent in the programming of the matrix. You are the eventuality of an anomaly which despite my sincerest efforts I have been unable to eliminate from what is otherwise a harmony of mathematical precision.....Architect: Precisely, as you are undoubtedly gathering the anomaly is systemic. Creating fluctuations in even the most simplistic equations....
Architect: ...she stumbled upon a solution whereby nearly 99 percent of all test subjects accepted the program as long as they were given a choice, even if they were [u][b]only aware of the choice at a near unconscious level.[u][b]
In these lines taken from the transcript of Neo's conversation with the architect we learn that the anomaly is caused by a mathmatical remainder that is left over from the programming that gives people a choice to believe the matrix. This remainder is "dumped" like a buffer overflow, or a call to stack dump in assembly language programming, and when it is, it is carried by a person. When they exit the Matrix to visit the source, the remainder is deleted from the programming and the equation balances back out. If it were not, then, quite feasably, everyone inside the matrix would become containers for the excess remainders causing chaos inside the matrix.
The mathmatical remainder itself, caused by the anomaly, is what gives Neo his abilities, not a cookie. Neo's birth in the matrix was most likely the mathmatical calculation that called the equation's "dump process" because the level that was reached - thus Neo becomes the anomaly.
We also learn here, the how and the why of the anomaly. Details pertinent to this subject - they have been discussed before and I don't feel like typing them again. Atleast not at this moment....