What VFX and video production softwares are used in movies like "Captain America: Civil War" and "Doctor Strange"?
This depends from Company to company, there are multiple companies working on multiple shots, or sometime even on the same shots. Because this (sometimes) differs a lot from eachother, it's really hard to give you an answer to this question.

As mentioned, this heavily depends on effects you want to acchieve and the company you work with.

These are some commonly used programms:


Cinema 4D 
BodyPaint 
AutoCAD 
3DS Max 
InfraWorks 
Maya 
Mudbox 
Flame 
Smoke 
Softimage 
Mental Ray 
Combustion 
FLIX 
MODO 
MARI 
NUKE 
OCULA 
HIERO 
Katana 
keylight 
Massive Prime 
Massive Jet 
Massiv for Maya 
Ready to run Agents 
Matchmover 
Z-Brush 
Adobe CS6 
Illustrator 
Photoshop 
Flash 
After effects 
Lightroom 
v-Ray for 3DS Max 
Rendermann  
Avid Media Composer 
Avid effects 
davinciresolve
Houdini
3D coat
topgun  
shotgun Studio  
PF Track 
NURBS 
Filemaker Pro 
vue 
Plant factory 
Ozone 
Carbon scatter 
Lumen RT 
Primatte 
ultimate 
Final Cut Pro 
Qube 
Synth-Eyes 
boujou 
Fusion 
3D equalizer 
Mantra 
Real Flow 
Fume FX  
BlueArc


I can narrow them down, if you can tell on which effect you are specifically interessted.