Here is a "not quite so obvious" flag. The euro and cent circulation coins from Austria do not have the country name but show the Austrian flag instead. This is, for example, the 10 cent coin (link only, but I have the piece): You will know that in heraldry the vertical stripes are the representation of red (if all you have is black and white), and the empty looking stripe is white. Thus three horizontal stripes in red, white, and red. Christian
In 2008 Finland issued a €10 collector coin dedicated to the 90th anniversary of the national flag. And while I do not really like colored coins, the color is used in a very subtle way here. Christian
1992 San Marino 20 lire celebrating the 500th anniversary of Columbus discovering the new world. Spanish flag.
British £2 coins from the 2002 Commonwealth Games - 4 different flags for England, Northern Ireland, Wales and Scotland. (The Northern Ireland one is the scarcest and most difficult to spot as the flag is the same as England but with "The Red Hand of Ulster" in the Cross.