First i think a perception filter would be amazing like in Doctor Who in season 5 episode 1 where he notices the hidden door in Amy ponds house but in minecraft lets say i walk into a house you know standard 3 roof high but there is this button :O hits it SUDDENLY THERE ARE 4 WHOLE NEW STORIES OF HOUSE but the perception only lifts for that person that hit that button 

A Teselecta You this could be a very good vech for Dalek mod kinda like the tardis but it shrinks you into the head and you can control your copy from there

Custom Sonic although probably brought up in past this would bring users close to the experience making there own sonic skin

A custom tardis Exterior as seen in dr who when Clara leaves the doctor the outa shell was a restaurant it would be cool to make your own outta Exterior

A diary that is bound to you like river song you can have a safe place to write those coords  in it and no one else can take them or use paper XD

A custom companion that you can put any skin on and you can tell it to fly your tardis to certain coords like  /companionflypos X ------- Y ------- Z------- and a return time at end if u want like  /companionflyreturnpos

A VORTEX MANIPULATOR this should be available for people without a tardis as in not hard to gather materials but it can only travel to the pos 

 here are some self explanatory ones

Dark water

Dimensional-Shift Bomb

Field Gravity Detector

Gravity globe

Home Box

Moment

Psychic paper

Security disk

Sonic cane

Sonic knife

Sonic lance

Sonic pen

TARDIS Compass

Terraforming device

Time Log

Time Lock

I like some ideas such as the personal Coordinates logbook. 

However some of your 'self-explanatory' suggestions aren't exactly self explanatory as it may seem. E.g. What does the Moment do in the mod? We know what it does in the show, but what's the function of it? Decorative?

I would reccomend  looking at these posts on how to post a suggestion:

Recommended Format: 

Posting Section 

List of features already confirmed 

Welcome to the forums

A great post for someone who's just joining the forums, although I do recommend "sectioning" the information a bit, bolding the names of the actual items for where they're first mentioned, and whatnot.

Anyway, welcome to the forums