There are several popularly used 3D Graphics/Animation software packages out there... Some easier to use then others... Same goes with Engines... Daz3D (most commonly used 3D Renderer, recommend watching tutorials for basic use, but may need classes or a book for the more complex uses, lots of pre-generated content to use/buy), Honey Select Studio/Neo (very popular, don't know much about it's usage beyond it having a ton of mods/plugin options, very hentai based), and there are others as well... The most popular Engines tend to be Ren'py (one of the easier engines to use, but still complex), Unity (very complex, very diverse usage, more prone to bugs due to complexity), RPG Maker (RPGM, somewhat in the middle on complexity, but is intended more for Role Playing Game mechanics over Visual Novel mechanics), Flash/HTML were very popular at one point in time (requires Flash creation software, and/or HTML creation software/programing knowledge), and there are lots of other not-so-commonly used engines as well...
And depending on what you plan to do, there are other general graphics editors you can use as well, such as GIMP 2 (free to use, lots of user generated tools available on the web, simple/complex depending on use), Photoshop (not free, commercial grade software, simple/complex/super-complex depending on use and version used), and there are lots of others...