Bane and Venom are brute forces and they could lay waste many, many, many, many men. I would even say Rhino, but Venom is far more superior.
Joker and Green Goblin just deserve to work with each other because they're both in the top of the food chain when it comes to their respected rogue gallery. No other villain on each side can top them.
Hugo Strange and Doc Ock mostly because, as I stated, of their intelligence levels. They don't really match in terms of fighting, but they're both extremely intelligent beings and they could really pull the strings. Now, they're pretty close number two to Joker and GG respectively, but they're still not the main-main villains, but they are both pretty freaking phenomenal.
Black Mask and Carnage works, for me, because BM can be very psychotic himself, so him pairing with Carnage could bring chaos all around. And the way Joker was shown in The Dark Knight is something I would have always showed Black Mask in a film, because I just think he could be this freakishly insane dude. And we all know Carnage is insane, let alone Cletus Kasady.
Scarecrow and Mysterio both literally ****s up Batman's and Spider-Man's minds. So...'nuff said on that, lol. I think Mysterio would be more helpful with Scarecrow than Carnage any day, imo.
Man-Bat and Man-Wolf are pretty much self-explanatory, lol. Literally a bat and a wolf...heck, I wouldn't mind bringing in Lizard with those two as well.
The next three(Firefly and Molten Man, Clayface and Sandman, Mr. Freeze and Hydro-Man) are just elemental ideas with their pairings. Reminds me of the Freeze and Firefly hook up on The Batman, so different elemental pairings of villains would be pretty awesome.