My plan is this.
I have developed a toxin deadly to Mary Sues but harmless to the average Joe. I've code-named it Lollipop-X.4, both for the sacharine sweetness of the Sues I despise and as a pun on Lollipop Guild/Munchkin. ("Munchkin", or "twink", is a term for a too-powerful character.)
Lollipop-X.4 works in several areas. It targets the protein effectors that regulate ocular colour-changing. It seeks out overtaxed scalp cells, such as might be seen with waist-length or longer hair. It also locks onto unnaturally high magical ability, as well as certain genetic markers proven to exist in the majority of Sues. Tests show Lollipop-X.4 is 99.2% effective in singling out Mary Sues - and more importantly, it never tests false positive, so powerful canon characters are completely safe.
All that remains is to administer the doses. This could be tricky to achieve, but I suggest that Legolas, Snape and various others be soaked in Lollipop-X.4 and then turned loose. Then all that remains is to sit back and watch the Sues drop like multi-coloured flies.