Aside from the quarters, there is also a special issue of the $2 coin issued in 1999 to recognize the creation of the new territory of Nunavut. This is not a Millennium coin, but since the Mint has been bringing out new coins all through 1999 and 2000, it could easily be mistaken for one. The Millennium $2 coin looks like a "regular toonie" but the bear now has cubs, and the coin has the words "Knowledge / Le Savoir" on either side of the polar bears. See it here.
No other coin designs were altered for 1999/2000.
BTW if you follow the above link, you will see that there is no mistaking the $2 coin for a quarter. Not only is it considerably bigger than a quarter (Canadian and American quarters are almost identical in diameter), it is bi-metallic: a centre of "aureate bronze" in a ring of nickel. The quarters are plain nickel.