Popular Software like Shake, Nuke, EyeOn Fusion are used extensively in the industry. Most of the blockbuster movies like Lord of the rings, Harry Potter, Cloverfield, King Kong, Fantastic four, Pirates of the Caribbean, Hulk, The Dark Night were done using these software. In most cases they are tweaked by the VFX companies to suit their needs.
Some of the top notch, state-of-the-art visual effects companies :
Industrial Light and magic (ILM) – Founded by George Lucas in 1975, it has be providing post-production visual effects services to the entertainment industry. http://www.ilm.com/
Sony pictures Imageworks - Los Angeles, California http://www.imageworks.com/
Rhythm and hues - Los Angeles, California http://www.rhythm.com/
Framestore – Working in digital film for over twenty years, it is the largest visual effects and computer animation studio is Europe. They worked on films like The Golden compass, Harry Potter. http://www.framestore.com/
Weta Digital – A world leading visual effects company based in Wellington, New Zealnad. http://www.wetafx.co.nz/
Soho VFX - Toronto and Los Angeles http://www.sohovfx.com/