Some institutions consider more than one credit card a bad thing, I believe that having more than two is considered quite negative.

Voluntarily closing a credit card is different to having one closed on you. For instance you apply for a new LOC at the bank, and they say you they will close your credit card to open it ... affects your score in a totally different way to you voluntarily closing a card.
These actions are associated with a reason ... closing a credit card should not negatively impact you, especially if you still have two other forms of revolving credit.