Defensive Threats:
Blissey - Infernape can smack it in the face with STAB Close Combat, Metagross can keep meteor mashing it or explode, Scizor can Superpower. far from a huge threat.
Bronzong - Infernape can Fire Blast it, Starmie can 2hko with Hydro Pump, Gyarados can basically force it to explode, where I can switch in something like Metagross to take the hit, or it can risk being KO'd from Waterfalls.
Celebi - Infernape, 2 U-turner's, an exploder, a choice band pursuit user, and powerful Ice Beams make Celebi far from a huge threat to me.
Cresselia - Scizor and Metagross can make pretty short work of it provided it isn't some weird Psycho Shift Burn Orb thing that I was up against once.
Dusknoir - I really like never see Dusknoir's, but if I did, it could sadly cause me some problems. I guess Starmie and Infernape can 2hko with Hydro Pump / Fire Blast respectfully, but that's about it.
Forretress - Infernape and Starmie can beat the piss out of it, provided they don't switch into an explosion or something or Infernape into an Earthquake. Gyara if he's set up is certainly taking him down after stealth rock.
Gliscor - Infernape, Starmie, Gyarados all easily take him down with powerful super effective hits.
Gyarados - Flygon can easily revenge kill with Thunder Punch, Metagross can take a hit and explode, Infernape can 2hko on the switch with Grass Knot, and Starmie can Thunderbolt it to oblivion.
Hippowdon - Infernape's Grass Knot, Metagross' Explosion, Starmie's Hydro Pump, and Gyarados' Waterfall all severely hurt, or ohko Hippowdon.
Jirachi - I'd just like to say I hate Jirachi, first of all. But then again, it really doesn't cause too much of a problem to my team, unless it's the calm mind sweeper, in which case I am basically screwed if it sets up.
Rotom-A - Yet another one of my problem pokemon, and the reason I was contemplating running Scarftar instead of Scarf Flygon. I really don't have much that can deal with Bulky Rotom unless you count Flygon being able to come in on Thunderbolt. =/
Skarmory - Starmie and Infernape both murder basically any skarmory.
Snorlax - Infernape can come in and Close Combat it, Scizor can Superpower it or U-Turn to a counter, and Metagross can blow up in his fat face.
Suicune - I tend to have a problem with Suicune's especially ones with HP Electric because i don't really have much that can take them down aside of Metagross exploding on them. or trying to outspeed the non-bulky ones and do something like have Flygon Outrage (Thunder Punch if it's low enough on HP) into it, then drop in Infernape to finish the job with Close Combat. A good Suicune counter would be appreciated.
Swampert - Infernape Grassknots and Starmie Hydro Pumps.
Tentacruel - Flygon can come in on a toxic spikes or rapid spin and OHKO it with Earthquake.
Tyranitar - I have pleanty of things that easily deal with Tyranitar, flygon's stabquake and rock resistance, scizor's bullet punch, starmie's hydro pump, and both of my scouter's U-Turns.
Vaporeon - Starmie can Thunderbolt it, and if it doesn't have ice beam, flygon can hopefully get in a few outrage hits and Thunder Punch it as well.
Zapdos - Starmie can hurt it pretty badly with Ice Beam, especially after stealth rock, flygon can switch in to anything except HP Ice and hit it really hard with Stone Edge, gyara can also run it over with stone edge provided he got the dance up and can definitely outrun it or hit it on the switch in.
Offensive Threats:
Azelf - if it's the lead, Starmie's Hydro Pump + Rapid Spin make short work of it and get rid of its stealth rock.
Breloom - Metagross can take the sleep with lum berry and smack it in the head with a meteor mash. and provided I got it out of its sub, starmie and infernape can both hit it really hard with super effective hits, also scizor can ko it with bullet punch.
Dragonite - the leads are dead meat to Starmie, but later in the game Flygon can outrage it for the OHKO even if it's jolly and got a dragon dance. Infernape can also OHKO it with HP Ice.
Electivire - Does anyone good honestly even use this thing? But uhm, Metagross can OHKO it with earthquake, and so can Gyarados if it gets it on the switch in or has a dance under his bealt and it isn't scarfed or something. I'm also pretty sure Infernape can OHKO it with Close Combat.
Gengar - scizor gets the non-sub/protect ones that carry HP Fire, starmie can ohko with hydro pump, gyara with a dance can outrun and ohko with waterfall.
Gyarados - Flygon can switch in to anything but Ice Fang and OHKO with Stone Edge after Stealth Rock.
Heatran - Gyarados can take pretty much anything it dishes out except explosion. Infernape can ohko it with close combat if it isn't choice scarfed, and starmie can do the same with hydro pump.
Heracross - Gyarados resists both stabs and intimidates it, so unless it stone edges on the switch, it's not doing anything to him, and it's also really uncommon. and if it's choiced (which they almost always are), I can still easily revenge kill it with just about anything on my team depending on what it used.
Infernape - Gyarados is my main infernape counter, being able to come in and intimidate on a resisted close combat and ohko with waterfall (or set up a dragon dance). Flygon can also come in on a fire attack or stone edge or something and ohko with Earthquake.
Jolteon - The only thing on my team that can take Specs Jolteon on is Flygon, and only if I'm switching in on Thunderbolt basically, so I can ohko with Earthquake. Basically I have a huge weakness to this thing.
Kingdra - can do a lot of damage to me if it's set up, but if it isn't yet, then I'll probably have to sack something to it so that I can revenge it. But flygon can come in on a dragon dance and ohko with outrage.
Lucario - Gyarados intimidates and resists it's close combat, and takes mediocre damage from most other things and can KO with earthquake
Machamp - Metagross gets 2 meteor mashes and doesn't care one bit about the confusion.
Magnezone - gyara outspeeds and ohkos with earthquake provided it isn't behind a sub, flygon earthquakes it, infernape gets it with fire blast and close combat, metagross can get it with earthquake unless it magnet rises, and scizor can ohko with superpower if I predict it I guess.
Mamoswine - Starmie OHKO's with Hydro Pump, Scizor OHKO's with Bullet Punch, Infernape OHKO's with either stab, Gyarados OHKO's with Waterfall, and metagross can ohko with meteor mash.
Metagross - provided it doesn't have an Occa or Shuca Berry a ton of my pokes can OHKO with Earthquake, and Infernape gets him with Fire Blast.
Salamence - Well he isn't on suspect, but when I'm playing standard OU, Metagross can switch in on Outrage, and so can Scizor, and both can smack the crap out of him. Gyara can stone edge it as it switches in and Infernape can HP Ice him in the face.
Scizor - Gyarados makes all except swords dancer's with quick attack basically set up fodder.
Starmie - Gyarados outruns and OHKOs non bulky versions with Earthquake. Scizor can lock it in place with Pursuit and OHKO as long as I survive a hydro pump. and I can also U-Turn it for some decent damage and switch in something to take the predicted attack from it.
Togekiss - Gyarados smacks his face in with Stone Edge, Scizor can repeatedly Bullet Punch it, Starmie can Ice Beam/Tbolt it, Flygon can come in on twave and Stone Edge.
Weavile - Scizor can come in on any of its attacks and OHKO with 3/4 of its attacks. Gyarados can also come in and intimidate it and set up a dance or just go for the ohko with stone edge.
Yanmega- can be a bit of a problem late game, but scizor can definitely make short work of him with Bullet Punch, and Gyarados can take a hit and OHKO with Stone Edge, same with Flygon.