The history: Perhaps out of fear, Bourdain is a little more careful with his Ramsay burns. He rarely outright rips him as a person -- in fact, he's said before that "Gordon's actually a really sweet, nice guy." But he called Ramsay's move to copyright Spotted Pig (and thereby screw over the owners of the renowned New York spot) "shameful pathetic." And he's very vocal about how much he hated Hell's Kitchen.
Have they made up? This is a pretty minor one, and Gordon thrives on this stuff, so they're probably fine. Even if there was no public mea culpa.
The history: There's an entire chapter in Medium Raw called, "Go Ask Alice" that takes Waters to task on her voting record, cooking credentials, and essentially her whole image. Bourdain's mad about all of it, but the gist of his rant is that Waters promotes this locally sourced, fresh food agenda without A) taking into low-income families, and B) worrying about sustainability.
Have they made up? Nope. Bourdain never really backed down, and Waters made a parody Twitter account because, as she put it, "Tony has always been something of an ass to me."