I always leave welkynd and varla stones right where they are. Same with nirnroot. As long as my games are, I know my character will be back to visit places, and we want them to look as nice as the first time.
This is one of the reasons I play multiple characters. Some of my characters would never dream of taking the pretty stones, while others will greedily seek them out. Likewise with the nirnroots. Characters interact with the world in their own ways, and the world becomes "theirs."
It's a wonderful feeling knowing that there's a pristine, untouched Cyrodiil as far away as the "NEW" choice on the Main Menu. There's always a living, breathing Emperor, just about to come down the prison stairs, and there are always Khajiit highwaymen lurking on the roadside up ahead.
And, at the same time, there are Cyrodiils scarred by the burned remains of dozens of Oblivion Gates, where a Champion owns several homes filled with treasure and plunder, and nobody has seen a nirnroot or welkynd stone for years, and those places are as close as the "LOAD" button...