I can't really think of too many sets that I'd like to see from Republic, Empire, or any other series, but here are quite a few from Clone Wars.
Star Wars Republic:
Star Corps Trooper vs. Morgukai Warrior (Siege of Saleucami Story Arc)
Clone Wars Adventures
Mace Windu and Battle Droid and half of Ultra Battle Droid (Volume 1: Heavy Metal Jedi)
Saesee Tiin and Clone Trooper and other half of Ultra Battle Droid (Volume 1: Heavy Metal Jedi)
Wookiee Warrior and Flamethrower Trooper (Volume 4:Descent)
Clone Commando Leader and Yellow ARC Trooper (Volume 4: Descent)
SA ARC Trooper and Viidaav Soldier (Volume 5: Heroes on Both Sides)
Clone Trooper Commander and Clone Trooper (Volume 5: The Order of Outcasts)
Joc Sah and Sergeant Remy (Volume 5: The Order of Outcasts)
Jedi Master Sev and Ragmar V Resistance Leader (Volume 5: The Order of Outcasts)
I really would like to post pictures, but I don't have a scanner, nor do I have the time to search for them. Sorry.