You might consider this system: Get several sets of color-coded dice. Each color represents one type of bonus (e.g. green = natural AC; blue = deflection; etc.). Each player who has a bonus of any given type keeps one die of the appropriate color set on his or her character sheet (or nearby, or whatever), with the value of the bonus set upright. In this way, each player has a running total of current bonuses at hand, which changes as the game changes. Simple and effective.
The trick occurs with the DM: How do you keep track of all those bonuses for all of the monsters/NPCs in the game? Maybe a laptop+spreadsheet for the DM (only) isn't a bad idea?