In the movie, Clarke gives a gift to his boss and all of the boxes are the exact same shape. Is it everyone hinted/explained what the gift was? And why they were all the same?
According to IMDB trivia, the gift was a desk organizer. To explain why, see this question and answer However, a desk organizer is still speculation as it isn't revealed in the movie. It may be somewhere in the script, though.
All the presents that were on the credenza when Clark went in to give his to Mr. Shirley are identically shaped, and likely the same gift. It is a desk organizer. When this movie came out, pen sets came in an L-shaped arrangement. The writing instruments were on the flat part, and the raised section held Post-It notes. Paper clips and other holders were also a possibility.