As it stands currently, there is no more use for tokens after a character has obtained the 1000 token board. It would be nice if additional tokens beyond 1000 could be "spent" to get IP reset points.
For example: for every 1000 additional tokens earned (number to be adjusted as appropriate), a character can receive one additional IP reset point.
This wouldn't be too overpowering because getting the required number of tokens isn't a trivial task. However, if you really wanted to reset a skill but didn't have any reset points left, and you are willing to work hard and earn the necessary tokens, then you can obtain an extra IP reset point with enough effort.
Since the mechanism for awarding and keeping track of tokens is already in the game, and an IP reset-point system is already in place as well, it is hopefully not too much extra work to implement. It might be done as a change to the 1000 token board item - for example, if you right-click on it, and you have at least 2000 tokens, then it will add one reset point to your reset point pool and subtract 1000 tokens from your token count. It'll give players a reward for earning tokens even after they get the 1000 token board.