What are the positive and negative effects of Charlie's surgery?
Some of the positives are that Charlie becomes a more productive member of society, Strauss and Nemur's research is progressing, and that this treatment might prove to be hopeful for future candidates.
Once Charlie gains his intelligence (and also before he returns to his "old" state), he is able to function as a "normal" human being - he is responsible, knowledgeable, and shows a determination to learn and develop. Also, the research makes a significant advancement, now that it has been tested on humans. Although it ultimately results in regression, it can now be studied further and perhaps improved to minimize or eliminate this threat in subsequent attempts.
As for the negatives, the test is not fully safe as of yet, as we see in both Algernon and Charlie. Also, it can be argued that this change in Charlie's intelligence causes changes in other people's lives - his co-workers can no longer mistreat him, he loses his job, Alice must question her own feelings, etc. (although this might not necessarily be considered a negative effect!). Finally, the adverse side effects prove to be quite dangerous.
Charlie's surgery has the positive effect of making him highly intelligent. His intellectual life explodes. He is able to learn a number of foreign languages, become advanced in mathematics, and increase his vocabulary. His whole world broadens.
His new intelligence means, as well, that he is able to have a mature relationship with a woman. He falls in love with Miss Kinnian. This offers him the possibility of a fuller emotional life than he had before. He also can engage in research into his own case of enhanced intelligence. He is able to recognize that Dr. Strauss and Dr. Nemur have limitations that he doesn't.
The downside is that he recognizes he has been used, like the mouse Algernon, as a "lab rat" by people who do not have his best interests at heart. He is also able to learn that he will lose his intelligence, and because of his intelligence, he understands the full tragedy of what that means.