Here's the ranking for the X series' weapons and their charged variants - I only did the SNES games as those were the only ones I've beat so far (be on the lookout for X4-6!). I used the same approach as with the Classic series, so check that out.
Since I've played A LOT of MegaMan over the past year or so, I thought I might rank (most of) the Classic series' special weapons. I used utility, damage output, ammo, and how much I liked using it, as deciding factors in each weapon's placement.