Recently, I've played board games in settings where someone decided to cooperate with someone else, even when the games didn't dictate any kind of cooperation or negotiation. This feels very unnatural to me, and can change the dynamics of the game completely. The rules go from simply being listed in the rulebook, with the assumption of everyone working in their own interest, to making the game open-ended.
A few weeks back, I was playing Munchkin, and toward the end of the game we ended up in a situation where two of the four players, Nate and Nick, just needed a final level to win the game. During Nate's turn, he had the opportunity to make a winning move by himself, but instead he asked Nick whether Nick would like to share the victory by making this winning move together, which Nick of course accepted. Had Nate not asked to cooperate, he hadn't won at all, because Nick had a card that could've messed up Nate's seemingly solid plan.
I experienced another example when playing Carcassonne. Then, two of the players negotiated that "I'll help you build that city if you'll help me get out of this tricky area".
I'm undecided as to whether this type of cooperation and negotiation makes games better or worse. On the one hand, it can change every game into being about cooperation, negotiation and rapport, which may be unfair to new members of a group and to those of us who are bad negotiators.
On the other hand, it makes a game richer, by adding a layer of informal, varying rules on top of the game's basic rules. Furthermore, cooperation and negotiation are important life skills that can be honed in the playful, non-critical, safe environment of games.