Asterix features the eponymous hero and Julius Caesar. Though the two of them are enemies—Asterix wants to keep the Undefeatable Little Village free of Roman rule and Caesar would like nothing better than to finally crush them and get that thorn out of his side—they have had several encounters where the two are functionally friendly to each other. Asterix treats Caesar with irreverent cordiality, which annoys Caesar to no end... yet privately Caesar still often finds himself admitting it's still better than dealing with the Senate.
The latter partly explains the Friendly Enemy relationship. Caesar may be the Big Bad, but he's surrounded by political rivals and ambitious underlingseager to take his throne, who are just as ambitious as Caesar while being nowhere near as skilled or as noble. Therefore, none of the Gauls really want him replaced, which leads to frequent Enemy Mine situations. Many stories are resolved either by the Gauls defeating one of Caesar's enemies, or by Caesar showing up and putting a stop to one of his underlings' plans against them.
Buck Danny has a relationship like this with a defecting Soviet pilot, who later turns out to be a false plant still operating under Soviet orders. During their last dogfight, he salutes Danny as a Worthy Opponent, while Danny, after shooting him down, mentally acknowledges that the man gave his life for his country and deserves nothing but respect for it.
Corto Maltese and Rasputin have this exact relationship. "I'll kill you one day, Corto. (...) You're missing out on a lot by not being my friend".
Disney Ducks Comic Universe: Scrooge McDuck usually has a surprisingly good relationship with his Rogues Gallery - especially the Beagle Boys and to a lesser degree John D. Rockerduck and Magica DeSpell. They seem to respect and care for each other on several occassions and team-up against greater threats. It doesn't stop with Scrooge: Donald and other relatives seem to get along with them pretty well too.
Donald Duck as Paperinik (both in the classic stories and in Paperinik New Adventures) has developed this kind of relationship with the lesser criminals of Duckburg, with the typical scene being of Paperinik catching them in the act and say hello, having a little chat, and the thieves then picking up everything and going to the closest police station to let themselves be arrested. The really interesting part is how it developed: the criminals are utterly terrified of Paperinik due the sadistic beatings he inflicts on everyone who tries and resists, but as he's also polite and nice when they're not committing crimes or resisting they started giving up as soon as he shows up, resulting in this strange friendship. He'll also defend them when some newcomer butts in and hurts the criminals unnecessarily.
In PKNA he and the Raider who rarely ever gets into direct conflict with Donald. In fact, he's more like a criminal that Donald has to ally himself with from time to time than an outright enemy.
Mickey Mouse Comic Universe: Mickey and Pete have a rather good relationship with each other despite being on opposing sides of the law. They even watch TV together on occassions. Chief O'Hara and Pete also are on very good terms with each others and will help each other out if necessary. Pete's criminal girlfriend Trudy also seems to get along well with Minnie, Mickey's fiancee.
The Sonic X comic book portrays Sonic's and Eggman's relationship as exactly this. When Eggman's not launching an Evil Plan, the two are practically friends. They have civilized conversations, face off in (mostly) friendly competitions...Sonic even helps Dr. Eggman get his secret lair back in control so he can get back to launching his evil plans again. When Eggman shows up for a party, no one bats an eye, either. Eggman's just the friendly neighborhood supervillain.
Sonic the Hedgehog (Archie Comics): While in the games, Sonic and Knuckles have been friendly rivals ever since Sonic & Knuckles, these comics typically presented Knuckles as "Sonic's friendly nemesis" instead due to their relationship being more antagonistic than in the games. Eventually, Knuckles got enough character development for the "Enemy" part to be dropped.
In the Transformers Generation 1 comic books, Optimus Prime and Scorponok (who was the Decepticon leader for most of the second half of the book's run) become this through a series of Enemy Mines.
In The Transformers (IDW), Optimus's relationship with Megatron is...complicated. At one point, when Megatron has surrendered as part of a plot, they start swapping old war stories about the times they had attempted to kill each other, trading jokes about the assorted injuries.
Optimus: Or — or the siege of Massungrad, when you- Megatron: When I trapped you in the antimatter chamber... Optimus: They practically had to stitch me back together from the blast patterns on the walls! ... Megatron: And what about Rada Mor, home to those sentient explosives you were so desperate to protect? I was reduced to cinders! They had to shovel me into the CR chamber! ... Optimus: Heh. Megatron: Heh.
Entombed from a Polish series WILQ – Superbohater (Wilq the Superhero) is categorized as a villain. However, he is also the protagonist's best buddy and most stories involve both of them solving the problem at hand as a team. The same applies to Alc-Man, who shares a similar relationship with Wilq and is also technically a villain. Neither of these two villains do much villainy, in contrast to Wilq's real enemies.
