I have some strong opinions on runs, for this tier list, only going to rank runs I've personally done, as I'll have more to back my opinion up on. Doesn't mean I have no opinion on other runs, nor does it mean I won't voice them. Will add justification at some point.

S
Colo - SALSA!!!

A
LGP
Blue CEA
FRR2
Yellow Glitchless

B
TCG - A tier except for how much mashing and grinding there is
FRLG Any%
LGE - worse LGP
XD - haven't experienced much of this game yet, may move up to A or down to C as I gain more experience
Moon
Crystal Glitchless (did a decent amount of practice and learning, haven't finished a run yet)

C
Red Glitchless
Gold Manipless
DP Glitched Manipless

D
Stadium
HGSS Manipless
Red Classic

F
Gold Glitched
Blue NSC
ORAS
Yellow Classic

Will Consider Sorting at Some Point
Emerald Glitchless (did a little bit of practice and learning at one point)
Plat Manipless (similar to Emerald, but technically finished 1 run)
BW Manipless (similar to above, easily the most likely of these 3 I'll actually run at some point)