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.