The rarest Transformers are not the actual production pieces, but variations of them. These can be quite subtle as a detail change to as a large as a complete color change.
Yellow Bumblejumper MOSC
Jazz Cookie Crisp Mail-Away
"Pepsi Prime" Optimus Prime Promo
Jetfire w/ Macross Symbols
Scourge Painted vs. Unpainted vs. Targetmaster
Cyclonus Painted vs. Unpainted
Oversized Tech Specs w/different readings
Nightbeat w/ Koren Stickers MISB
"Blue & White" Huffer
Optimus Prime w/ "Red Feet"
Red Tracks "MB" w/ Styro Inserts MIB
Ratchet "MB" w/ Styro Inserts MIB
Mirage "MB" w/ Styro Inserts MIB
Prowl "MB" w/ Styro Inserts MIB
Wheeljack "MB" w/ Styro Inserts MIB
"Red Faced" Twin Twist
"Blue" Cliffjumper MOSC
"Purple Nosecone" Skywarp
"Metallic Maroon" Ramjet
Brazilian Transformers Section
Argentina Transformers Section
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