I've got my fair share of strange habits:
1.) I light symmetrically, especially when working with symmetrical things. I place torches every 4th, 6th, or 8th block or any other specific pattern that works depending on the area but always matching with the entire facility. In caves I place more sporadically.
2.) I place torches always to my right. This is actually so that I can always find my way out of a cave. It's a trail of breadcrumbs, if you will. There is always exactly one path with torches on the left: the path that leads back to where I started. When placing torches on the right side wall provides insufficient lighting, I supplement with floor torches.
3.) When exploring outdoors, I leave a tower 10-25 blocks high near every major landmark, in a place where it is visible from a large distance away. I try to make every landmark slightly different. For NPC villages I give each one a special monument with a theme befitting the name I have given the village.
4.) I name my most important landmarks, and landmarks near each other often share names, for example 'Distant Desert' Village, 'Distant Desert' Waystation, 'Distant Desert' Temple, or even 'Distant Temple' Waystation inside the temple. 'Spite' Nether Portal (inside 'Distant Desert' Temple) is named, as with all Nether Portals, by its Nether-side location. It exists within Spite Cavern which as of yet has no other significant landmarks.
5.) When exploring abandoned mineshafts, I place exactly one torch per segment, between the mineposts. All segments lacking a right side wall get a torch on the floor in the middle. I then clean up all of the excess stone blocks on the ceiling, fix broken mineposts, tear down the wood planks on shafts, and use those planks to build stairwells on shafts that actually go anywhere. Then I pick up all of the rail segments and naturally-spawned torches but I leave the cobwebs (cause I don't have silk touch shears). So that makes unexplored mineshaft distinguishable from mineshaft I have been in. And finally when I clear a segment, I place one wood plank at the front of it so I know it's clear.
6.) When I come across waterfalls and lavafalls, I try to plug them up, not caring if I delete the source block. When I find lava pools, I try to dig all the lava out either by dumping in gravel, scooping the lava into a bucket, or a combination of the two--to reveal the stone underneath. I always carry a water bucket and sometimes pour water on top and dig up the obsidian, but that method is slower.
7.) Nearly all of my houses, rooms, and structures are underground. I actually never thought about this or noticed that it was strange until I saw other people making houses on top of the ground. I think you people are strange and I am normal. After all, I often use already-existing caves to make my houses. That way they have a unique layout and I don't have to put effort into designing the base plan. I just touch them up here and there.
8.) I build nether portals to go to my distant locations. Not necessarily strange so much as travel-oriented. I just find some things aren't available nearby and I may have to go a long ways away to reach them.
9.) A strange thing I was doing for a while: I had a diamond pick with silk touch so I was taking it with me everywhere and picking up ores with it. I took the ores home and set them down to scoop up with my fortune pick, or if I was lazy I just threw em in the furnace. I was usually carrying a stack of coal ore so in abandoned mineshafts I left coal ore instead of a plank at the front of any segment that had coal ore left to mine but nothing else to see in it. I also was placing stone in the holes where I dug out ores, making caves appear to have naturally spawned with no ores, giving them a bizarre appearance. I learned the hard way that I can't be using stone to fill in lava as I can't tell the difference between natural blocks and the ones I placed. I stopped using this pick when I discovered the only way to repair it is with 1-2 diamonds at a time--it's cost is 42 levels when using an unenchanted pick. Unfortunately my new pick has the same cost even though I got it first try with 24 levels on the enchanting table. >.< Efficiency III, Unbreaking III, Fortune II -- It might be creating more diamonds than it's destroying though. I found 14 diamond ore and got 24 diamonds out of em.
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I want ocean content(thanks Möjang!), nether biomes(again thanks!!), and savanna passive mobs (meerkats incoming!?).