since this list is supposed to create a discussion I think it would be beneficial if we explained additions or removals. I was pretty conservative with eliminating Pokemon since I think we should (as a community) make sure that this list is as accurate as possible.
it's pretty obvious that some of these Pokemon are easily dispatched by the appropriate Hidden Power, but since Raikou can't have Hidden Power Grass / Water / Ice at the same time, I left those Pokemon in.
red means I don't think it is a counter / check and there are explanations below.
green means it is not a counter, i.e. either (a) it is easily killed by the appropriate Hidden Power (note that this does not include Venusaur, who can still “beat” HP Ice Raikou if EVed properly (b) it can only force out Raikou once at large cost to itself.
blue means it is a counter, not just a check if Raikou doesn't have a Sub.
black just means it's a check.
I'm using 68 HP / 116 SpA / 72 SpD / 252 Spe Timid as Raikou's spread which probably biases the calcs towards the check / counter because Raikou could pretty easily shift that SpD into SpA, or even some HP (since none of them *almost* kill Raikou).
Pokemon that can be used to counter or check Raikou on offensive / bulky offensive teams:
Dugtrio, Sceptile, Swellow, Rhyperior, Gallade, Hariyama, Hitmontop, Hitmonlee, Ambipom, Ampharos, Swellow, Venusaur, Nidoking, Leafeon, Alakazam, Regirock, Torterra, Mesprit, Electrode, Camerupt, Shedinja, Raikou, Steelix (added).
Gallade
is slower and must use Close Combat to break Substitutes (or risk misses); easily 2HKOed at +1 or OHKOed with a CC SpD drop.
+1 Thunderbolt vs 0/0 Gallade 442 Atk vs 266 Def & 277 HP (95 Base Power): 169 - 201 (61.01% - 72.56%)
+1 Thunderbolt vs 0/0 -1 Gallade 442 Atk vs 177 Def & 277 HP (95 Base Power): 255 - 301 (92.06% - 108.66%)
Ampharos
set up bait. if it has Focus Punch, the best it can do is probably to die while ensuring Raikou doesn't have a free Substitute up. I didn't use any calculations but Ampharos is basically a special attacker with a weak Focus Punch for Clefable / Chansey, so...
Leafeon
horrible SpD and HP and can't OHKO Raikou even after it Substitutes with a Jolly LO Leaf Blade – maybe a shaky check to get Raikou weakened in a pinch but is still 2HKOed by a +1 Thunderbolt.
+1 Thunderbolt vs 0/0 Leafeon 442 Atk vs 166 Def & 271 HP (95 Base Power): 135 - 160 (49.82% - 59.04%)
+1 HP Ice vs 0/0 Leafeon 442 Atk vs 166 Def & 271 HP (70 Base Power): 268 - 316 (98.89% - 116.61%)
Jolly LO Leaf Blade vs 68/0 Raikou 319 Atk vs 186 Def & 338 HP (90 Base Power): 216 - 255 (63.91% - 75.44%)
Mesprit
can't kill Raikou, and doesn't even weaken it enough to get it into easy revenge kill range. easily 2HKOed by +1 Thunderbolt and if it invests more in defenses it doesn't do as much with Zen Headbutt.
Jolly Zen Headbutt vs 68/0 Raikou 309 Atk vs 186 Def & 338 HP (80 Base Power): 144 - 169 (42.60% - 50.00%)
+1 Thunderbolt vs 0/0 Mesprit 442 Atk vs 246 Def & 301 HP (95 Base Power): 184 - 217 (61.13% - 72.09%)
Pokemon that can be used to counter or check Raikou on balanced-to-stall teams:
Chansey, Donphan, Clefable, all the Regis, Rhyperior, Umbreon, Steelix, Venusaur, Hariyama, Nidoqueen, Tangrowth, Claydol, Lanturn, Ampharos, Gastrodon, Lickilicky, Quagsire, Cradily, Shuckle, Torterra.
Lanturn
set up bait for Sub / CM. I don't think damage calculations are needed...