Hmmm...quite a simple thought, yet so intriguing! I like using both, and I can see the unique use of each office tool, but I must say that I favor staples most times. I say "most times", because I think that depending on the purpose which I have assigned to the document that I am seeking to bind together, then I think that would influence my choice between using a paper clip to do the job, or simply stapling it. I think that when one has chosen to staple something, it suggests permanency, in that you are certain that you want these two or more documents to be bound together, and you are not thinking of separating them from each other any time soon. On the other hand, when you choose to use a paper clip, then it hints that you either cannot find staples if your intention was to bind them permanently/B], or that you intend to separate the documents in question, in short order. I'm a "staples person", but paper clips have their special use and function, so respect must be given to both, and use made of them!
It depends on the papers I'm using it with. If they need to be stuck together forever like a 2 page resume or something, I tend to staple them but for just the purpose of keeping them tight and in order I use paper clips.