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So far I've found

Scaling Holograms (1WTC informed me on this) (Version: 1.8)

• Do /blockdata and set the coordinates on the hologram
• Modifying the "scale" tag should allow you to change the size of the hologram

Chanhging the particle Effect of a floor grating (1WTC informed me on this) (Version 1.8)

• If you do /blockdata, you can You can change the particle effect which comes out of a floor grate by changing it's ID in the block NBT Data (1.8)

Solid Holograms (read this somewhere in the forums. I forgot where) (Version: 1.8 | Untested on other Versions)

• Rename the Hologram on an anvil: "< Name of player  >:1"

Arcade Machine Block (Version 1.7.10)

• Doe_Killer informed me on it. I'm not sure how it's obtained though

Shell and Mod Division References (Version: 1.7.2)

• I forgot how I found these. I'll check and update this later 

Scaling Tardises (Version: 1.8 | Untested on other Versions)

• Place a Tardis at your feet and type /blockdata ~ ~ ~ {scale: < number of your choice >.< number of your choice >f}
• Someone asked about this recently. I hope I've answered your question

Changing the Pacticle coming from the floor grates (1WTC informed me of this) (Version 1.8)

• I had trouble finding it in the creative inventor, so I did /give < player name > thedalekmod:bFloorGrate
• Stand on the plate and do /blockdata ~ ~ ~ {pid:< id of your choice >)}
• The Particles coming from the floor grate will change

Skinpacks (Not as much of a Secret, but it's also not something that's obvious) (Version: 1.7.10 & Version 1.8 | Untested on other Versions)

• Pressing the P button will activate it

Working(ish) Delorean (Version: 1.7.10| Untested in other Versions)

• Doing /summon Delorean will summon a Bessie Reskinned to look like the Deleorean
• The "Working" means it drives and all (in contrast to the one in the 1.8 version, which is just a model)
• The Ish part means that it does not Time travel.

Credit: I found this through the Fanmade and Unofficial Dalek Mod Wiki

Gravity Falls Cart (Version: 1.7.10| Untested in other Versions)

• Doing /summon DMGFCart

Credit: I found this through the Fanmade and Unofficial Dalek Mod Wiki 

Dalek Mod Command window (Version: 1.7.10)

(50ap5ud5 found the 1.7.10 one. For the 1.7.2 one, it was someone on the Minecraft Forums thread. I can't remember who)

• Press the "P" button in game (or "O")
• Commands:
  • Unknown atm
• There's something similar in 1.7.2, but I forget if it's the same one

The following are from 1WTC himself:

Glenn Miller (Saym face) is in the Sun on Gallifrey (1.7)

• Here's a video on it

Companion Naming (Version: 1.7)

• Rename a companion "johnjohn24" and killing it will play the Windows XP shutdown sound
• Renaming a companion "UDWF1" and killing it will  spawn lots of sheep

 Giant Dalek (Version: Early 1.7 builds, 1.7.2)

• Renaming a Special Weapons Dalek "SWD" or "1WTC" in an early 1.7 build will make it giant

Member Specific things

• 1WTC looks like Tinfoilbot from Roblox (1.7)
• When playing as 1WTC or RedDash16 if you shift click with the sonic it will display a list of all players on the server and there position, this was added in late 1.6 so John and John could locate Sams secret island on the old Dalek Mod Server (1.6+)
• There is an item in the 1.8 version of the mod called "Black Box" this is modeled after the Black Box from TF2 and can only be used by 1WTC, RedDash16 and Hughpugh (1.8)

Notarocketlauncher (Version: 1.7)

• There is an item which looks like a credit but is actually a rocket launcher (1.7)
• You can find this using commands or TooManyItems
• Presumedly, it's the predeccessor of the Black Box
  • Unlike the Black Box, however, anyone is allowed to use this

PC Block (Version: "the development builds of 1.7")

• Obtained with /give thedalekmod.pc (I was informed of this by doe_killer)

Statue of 1WTC dressed in John Lennons Sgt pepper outfit (Version: 1.7)

• Obtained with /give thedalekmod.SgtJohn (I was informed of this by doe_killer)

Weeping Angel Head Block (Version: 1.7)

• Obtained with /give thedalekmod.golfCart (I was informed of this by doe_killer)

 Dalek Mod Story Mode? (Version: Idk)

• Up until recently old Modloader story mode files were left in the Dalek Mod assets directory

Minecraft Pocket Edition (Version 1.7.10)

• Using some mods you can access Minecraft Pocket Edition

Christmas Advent 2013:

 If you, like me, came a bit later you probably didn't know about the 2014 Advent calendar.

Usually, SWD puts everything in the mod that, well, is normally in the mod, 

but in this version of the Dalek Mod, the Christmas Advent things had to be downloaded from UDWF1's videos

Notably, many of  these things never were ported and many weren't in the version itself.

So, unless you knew or were informed, you may never have known about these things 

There is a thread on it here link

 If anyone else has anything to add just reply below

 IVE BEEN LOOKING FOR THAT FOR AGES!!! TY

Found out only staff can use the blockdata command

 Don't forget the secret skin packs

 What skinpacks are you referring to? The ones you access by pressing "P" are a known feature of the mod.

 Yes

 Well, they aren't really "Secret" per se (as they are widely known of), but I guess they could be a bit secret if you aren't told of them in advance and are new to the mod (I honestly stumbled upon them by accident when I first learned about them) :P

Just to let you know, I believe skinpacks were added in U39 for 1.7.10 and then ported up for the 1.8 DM. They weren't in older versions like 1.6.4.

#BRINGBACKTHEGOLFCART

Here are a few more secrets:

• Glenn Miller (Saym face) is in the Sun on Gallifrey (1.7)
• There is a PC in the development builds of 1.7
• There is a Statue of me dressed in John Lennons Sgt pepper outfit (1.7)
• There is a Weeping Angel head block  (1.7)
• Rename a companion "johnjohn24" and kill it, it will play the Windows XP shutdown sound (1.7)
• Rename a companion "UDWF1" and kill it, it will spawn lots of sheep (1.7)
• Using some mods you can access Minecraft PE (1.7)
• 1WTC looks like Tinfoilbot from Roblox (1.7)
• When playing as 1WTC or RedDash16 if you shift click with the sonic it will display a list of all players on the server and there position, this was added in late 1.6 so me and John could locate Sams secret island on the old Dalek Mod Server (1.6+)
• Renaming a Special Weapons Dalek "SWD" or "1WTC" in an early 1.7 build will make it giant (1.7.2)
• There is an item which looks like a credit but is actually a rocket launcher (1.7)
• Up until recently old Modloader story mode files were left in the Dalek Mod assets directory
• There is an item in the 1.8 version of the mod called "Black Box" this is modeled after the Black Box from TF2 and can only be used by 1WTC, RedDash16 and Hughpugh (1.8)
• You can change the particle effect which comes out of a floor grate by changing it's ID in the block NBT Data (1.8)
• Using the scale NBT Tag you can change the size of holograms.

 NBT tag? Where can I find that ?

You can edit the NBT stuff using /blockdata

 Thank you.

I'll start adding these to the thread

I've never played Roblox, so 1WTC means this right?

https://youtu.be/TSznTdj0E6I?t=2m34s

Also, I added the information on the Old advent Calendar

 https://youtu.be/TSznTdj0E6I I think it's this, though i haven't played much Roblox myself