The gold standard
Conventional wisdom says that the best way to honor an athlete after his or her career is to retire their jersey number. In this case, conventional wisdom is wrong on two counts. First off, there are only so many numbers you can retire before you have zero numbers left, and it's also a poor way to honor the greatest players to wear such a uniform.
The best way to honor a great player is to instill in the athletes what it means to wear the number worn by a legend. At Notre Dame, players are given a card with the legends who have worn their particular number, and they don't retire any number regardless of how legendary of a career that player has had, and it makes sense. If Notre Dame started retiring numbers, they would have no numbers left, and would also have to disrespect great players by not retiring their jersey. My New York Giants ran into this exact problem with Harry Carson, who is a Hall of Famer, but every week, a player lines up wearing his number 53 jersey despite the fact that some lesser Giants have had their numbers retired. This is simply an inequitable system and it cannot be sustained over a long period of time.
At Syracuse, their #44 was worn by Jim Brown, Ernie Davis and Floyd Little, three of the greatest players in the history of college football, and thus: the number has a special meaning to the point where there is even a blog named in its honor. There would be no better honor to the legacies of those three men than to allow someone else to wear 44 for their senior season, and retiring it permanently was a stupid decision made by a bunch of bean counters to sell jersies and t-shirts.
If you instill tradition, and adequately give respect to the prior wearers of the numbers in question that there is no greater way to honor a player than to allow him to wear the number of an all-time great. If no one on a particular team is worthy, hold the number until there is a player who is worthy, but never unequivocally retire a number.