I2C is slowly becoming the most used digital communication protocol on new generations devices (eg: sensors). And I'm pretty sure well see more and more devices coming out using this protocol.
It would be smart to mark these pins with "SDA" and "SCL" on the silkscreen so that users know where to connect their devices.
Instead of on the silkscreen as it becomes rather full with text I can imagine that the IDE could provide this kind of information in a separate help topic. Help > Hardware or so.
Stickers or something like that is a good idea. I have been working with TWI/SPI a bit. For performance reasons I also have been working a lot with the ports directly instead of using the Arduino libraries. I find it frustrating to constantly look up and cross reference the Atmega pins, Ports, and their functions with both the Arduino Uno and Arduino Mega.
With all the information that I have been using, there is not enough board space to print the information on the board. Using a sticker or overlay that can be swapped out depending on what you are doing would be an excellent idea.