There are some who would argue that when something, intended or not, becomes so integrated into a game's meta as to be commonplace, you can't really call it an exploit. Iron golems were obviously never intended to be used as an unlimited source of iron for players who know weird tricks to farm them, but then iron farms became so popular Mojang decided to leave the behavior as is. Emergent gameplay is all well and good, but this essentially makes gathering iron completely useless; it doesn't just allow for iron farming, it incentivizes it. There isn't any reason not to use an exploit like this once you know it exists, even if it takes away from what would otherwise be an interesting part of the game.

...Rant aside, these sort of things have been bugging me for awhile, so this afternoon I whipped up a lightweight little mod that blocks various exploits. Each of these is configurable with gamerules, (if you're really fond of MLG waterbucketing, you can leave it in, I guess), and I would just like to point out that it is perfectly within Mojang's ability to make these sorts of things configurable on their end, so there's at least the option not to be tempted by easy exploits. Just saying.

• Water Buckets, Snow Buckets, and Fish Buckets can no longer be used in midair. Using a bucket in midair instead drops it as an item. (Set to true by default.)
• Iron Golems no longer drop Iron ingots. (This can be configured as a percent chance of dropping Iron, and is set to zero by default.) They now drop iron nuggets by default.
• Players still take fall damage when falling in a boat, or in a minecart that does not land on rails.
• Mounting an entity while in midair no longer breaks a player's fall. (Instead dealing half fall damage to the player and the mount. Set to true by default.)
• Withers can no longer be trapped in bedrock or obsidian.
• Aggravated mobs can no longer be captured in boats. (This behavior works as normal, but if a mob is aggroed on a player, it will attack a boat or minecart it's trapped in in order to escape. Set to true by default.)
• Doors and other non-solid non-waterloggable blocks can no longer be used to create portable air pockets underwater. Placing doors or similar blocks with a water source adjacent immedieately breaks and drops the block.
• The Nether Roof is now off limits; entities that go above it teleport back below. (In order to encourage the challenge of actually building in the nether instead of ignoring it completely, and to nerf gold farming.)