I got quite a few...
On the side of the Evil Autobots
Energon Cliffjumper is Beachcomber
Universe Nemesis Prime + Shadow Commander is Ultra Magnus, at least until the official one shows up
Energon Doom-Lock is Slag
Cybertron Brimstone is Swoop
Robotmasters Dark Star Saber and Victory Leo are Dark Saber and Dread Leo respectively
Cybertron Dirt Boss is Kup
Robot Masters Road Rocket is Groove
TFTM Clocker is Windcharger
TFTM Storm Surge is SeaSpray
And on the Heroic Decepticons I have...
Energon Six-Shot is Shockwave
3 Botcon Sweeps is/are Scourge (sort of canon, but in my interpretation Scourge's mind is a shared conciousness)
Universe Dirge (Cybertron SS repaint) is Skywarp
Cybertron Red Starscream is Thundercracker
Legends Bumblebee and Cliffjumper are Runamuck and Runabout (or vice versa)
Cybertron Tank Unicron is Skullgrin
Classics Astrotrain (white one) is Astrotrain
G2 Laser Prime - Ultra Magnus recolour is Nemesis Prime (aka Bizarro Prime)
Kiss Players Cassettes are Flipsides (Decepticon guise) Laserbeak and Ravage (the "official" SG Ravage got a con label on him as is filling the role of Classics Glit)
Cybertron Snarl is Carnivac
Galaxy Force Black Fang Wolf is Wierdwolf.
as for who are "official" repurposes - there's a TFWiki article which is rather inclusive, and I have most of those too. I'd link you to it, but it's not responding at the moment.Ahh, now the link is working