Red tokens are awarded for scanning enemies/items, blue tokens for scanning lore and accomplishing side tasks and gold tokens are given for beating bosses on various difficulties. You can use tokens to unlock hidden content via an extras menu.
One example given is saving a pair of GF troopers from being killed, which pops up a blue token at the top of the screen for your "achievement".
The most interesting token of all is a "friends voucher", which you can send to your Wii comrades to unlock green tokens for both parties. Apparently this is more of a competition thing than unlocking actual game content.
