In a homebrew PF campaign, our party was captured in a secret underground prison, and had to break out. We decided that it should be done stealthily, which for our group translated to "kill things quickly and hide the bodies!" since the dwarven fighter boasted the best stealth. We decided the best place to hide the bodies was our cell, which worked well for us, but not as well for the only guard we knocked out and had chained to the wall. He woke up some hours later, neck-deep in a pile of his dead friends. According to the DM, no-one came to set him free, so he eventually died.
Same campaign, we were tracking down the "leader" (or so we thought) of the group that captured us. Our search lead us to a large underground lake. It took us about an hour of rowing to cross, but we did and found the lair. Miraculously, 2 of our enemies survived, including the "leader". We stripped them down, tied them together spooning each other, put them in a raft, and gently pushed them into the underground lake. So we left two naked dwarved bound together in a raft in the middle of a huge underground lake that is populated by scrags (yeah, we fought one). I'm not sure how we retained our Chaotic Neutral (or in my case, Chaotic Good) alignments in that campaign.
Not cruel necessarily, but definitely the most evil thing I have done. In a different campaign, using a somewhat modified 4e setting, I played a cleric. He was a standard heal/buff bot, and was welcomed with open arms. We eventually ran afoul of a super-powerful evil dragon, who my cleric made friends with by inviting him to afternoon tea. We found a tea shop that sold delicious pastries. Since the primary benefactor of the entire town was the evil dragon, it sold a number of oddities in addition to the more mundane fare. These treats were things such as meat-pies made out of orphans, or blood-filled donuts (from only the most innocent of virgins). Our party loaded up on our favorite pastries, with the evil warlock buying extra of the orphan pies. Pretty soon a new game had started. The warlock would offer the paladin a meat pie, promise him it was not made out of orphans, succeed at the Bluff check (the paladin had no Sense Motive), and make the paladin feel horrible. The game didn't last too long, as my cleric helpfully stepped in. With his higher Sense Motive, he was able to spare the paladin, and would intercept and replace the meat pies with ones from his own pack, that he had blessed to make extra tasty. The thing was, no one had paid attention to what pastries my cleric had bought. They were all worse than the warlock's purchases. So every time the paladin thanked me for saving him from having to do penance for cannibalism, I was feeding him orphan meat infused with necrotic energies. It was an experiment of some sorts, to see if I could force the paladin to fall via eating habits, a worthy quest for knowledge for a cleric who secretly worshiped Vecna. Unfortunately the campaign ended right as my plans came to fruition and a portal to another plane opened from the paladin's stomach.
Otherwise, I am in the same boat as many other on the thread. When I DM, I am far more cruel than my players are. I think some of them are still wary of me from Council of Thieves, where I spiced it up by adding traitors, and killing off almost all the NPCs they cared about. The Children of Westcrown Massacre was particularly horrifying to them, as I think only 3/10 of the NPCs survived, and most died horribly off-screen.