Here is a short list of external programs for Minecraft that I’ve used and can recommend personally. External programs are not mods and generally work with all versions of Minecraft.
NBTExplorer - Low-level editor for Minecraft’s NBT format. Can be used to make very precise edits and to learn about the format of Minecraft’s saved games. NBTExplorer has been essential to developing MCEdit.
World Painter - 2D world generator and editor that works based on height maps. Intended for making new worlds from scratch. Supports .schematic files from MCEdit and .bo2 biome objects from TerrainControl.
MultiMC - Minecraft launcher. Creates different “instances” of Minecraft, each with its own Minecraft version and collection of mods. Great for creating custom modpacks and has support for launching MCEdit.
Minecraft Note Block Studio - Compose music using note blocks! Supports importing .MIDI files and exporting .schematic files.
Here are a few mods that can use MCEdit’s .schematic files in some way.
WorldEdit - In-game world editor. Shares many features with MCEdit and has a few unique features of its own, including CraftScripts and mathematical function evaluation.
Schematica - Imports a .schematic file as a ghost outline for you to build yourself!
RecurrentComplex - Inserts custom-built structures into the world generator to be created naturally.