Here is a list of links to potentially useful software.
Digital micrograph - Gatan software for TEM data acquisition and analysis - Free basic version available (no EELS or EDX analysis).
DM scripts - Database of user written scripts for digital micrograph maintained by Dave Mitchell of the University of Wollongong, Australia.
HyperSpy - Python based multi-dimensional data-analysis specifically for EELS and EDX. - Open Source.
Atomic visualisation software
VESTA - 3D visualization program for structural models. - Free for non-commercial use.
Image and Diffraction simulation software
EMAPS- A suite of simulation software for diffraction simulation using Bloch wave or multislice. QED (Quantitative Electron Diffraction) is useful to simulate kikuchi patterns of a given zone axis.
CrystDiff - An interactive program for simulating electron diffraction patterns. Simple program to do kinematical simulations of single crystal electron diffraction.