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.