Attempted fix for CPU usage issue on single- and multiplayer.
Sometimes when you open a world you can get stuck for a short time (about 0.10 seconds).
Entering and exiting the nether in SMP resets health bar, but not health.
Dropped tools, once picked up, disappear after first use . Also if you die your tools can suffer a similar fate. If you shift-transfer such a dropped tool into a chest and back in your inventory, it's like a new-crafted tool without uses.
Holding a map in a boat can cause the arms to be misplaced. This can be fixed by exiting the boat, and opening your inventory. 
If a player sleeps in a bed, sometimes the bed is listed as occupied (even though it isn't) and, upon logging out, there is a NullPointerException and the player's .dat file is corrupted. There is an end of stream error when the player tries to log back in and their .dat file needs to be restored from a backup. This can be fixed by changing the sleeping value in the player's .dat file from 1 back to 0; this solves the issue and the player can then log back in. (You have to un-gzip the .dat file first, otherwise the file just looks like gibberish)
If a player crashes in the nether in SMP, some times when they reconnect, they spawn on top of the Nether. The only way back is death, or using teleportation.
Sometimes freezes most water into ice regardless of if its in a snow biome or not.
CPU issue fix is still failing, same loop as 1.6.3
Sometimes blocks will fail to render, creating massive holes on the ground and walls, allowing the player to see caves and dungeons under the map.  
Achievement display is sometimes off-panel. 
Updating of lighting due to Torches and other player instigated sources seems to be even worse.
Underground or otherwise enclosed Rail corners can cause you to clip through wall and lose health.
Minecarts colliding on the same track will pass through each other or come to a dead stop rather than pushing.
One Minecart may partially pass through another on a slope, when held by a non-activated booster track.  
Powered Minecarts do not push other Minecarts around. image gallery show problem, reversed image order
Exiting a Minecart or moving from one Minecart to another will bump the original Minecart and make it move.
Fire does not show up on a map item.
Fire sticks around much longer on blocks it can't burn.
Cobweb now acting like a solid block, player can pass through it, but he/she will get damaged.
You are able to travel down through a "closed" Trapdoor/Hatch (Under certain circumstances).
If the player is crouched while saving, he/she will then (when loading the world) spawn an additional 1.62 meters higher, and visibly fall to the ground (unhurt). However, if this occurs while standing under a solid block (such as a low ceiling), then the player will suffer 0.5 hearts of damage from clipping into the block temporarily ("suffocation"). Warning, also occasionally happens even when not crouched! (See Bug Report.)
When boats are submerged, they do not float back to surface. 
All TNT-entities stay client-side after exploding, until reconnection. (New bug because before just random ones stayed)
Shift-clicking to transfer items to/from chests, dispensers and storage minecarts can result in the game crashing if the items' destination would become full, or if there is no room for the new item.
Can't move and can mostly only see sky and sea when server.properties "view-distance" is set above 5. Note that the default is 10.
Hostile mobs sometimes spawn when using a bed even in a well lit room sealed off from outside environments, this appears to possibly be related to the lighting bug mentioned above (this can be an old bug: see ). Double doors also cause this to happen, the game somehow ignores one of the doors allowing mobs to spawn inside.
Craftable maps sometimes don't display the correct name, become blank or have gaps.
When crafting an item, shift clicking may cause different items to be created if the elimination of resources would create a situation in which that item can be crafted. For example, having 1 stone in the top left and two in the top middle and top right, along with two sticks in the middle and bottom middle, shift clicking will create a pick and a hoe.
When riding a boat with a map out, the player sometimes dies for no apparent reason.
Light bugs found in 1.6.2 can now occur in old generated chunks (not only in those generated in 1.6.x). Some screens here.
When climbing a ladder in a 1x2 shaft, under certain circumstances, it is impossible to target a block opposite of the ladder. The cursor will repeatedly alternate between the wall and another block, usually the ladder.
The corruption of world when running out of memory fix does not always work.
When entering and leaving nether life is shown incorrectly as full.
Maps may cause crashes or instability on multiplayer servers. When maps are used the server usually crashes in the same way: CPU usage goes to 100% and short after the server kicks all player and stops responding. <-- When I set view distance to 5, I could not open a chest with a map out. Changing it back to 10 fixed this bug.
Mushrooms can spread through walls.
Lava, in SMP, anywhere near wood, even if blocked by glass, will set the wood on fire. Have observed wood catching alight that is 10 blocks away from the lava source.
Maps sometimes stop updating the player position.
Spawn locations do not change when you sleep. (?)
Spawn locations may randomly shift large distances (?)
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