Here is a list of links to potentially useful software.

Data analysis

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.

ImageJ - Java based image processing program with a large number of user written plugins available. - 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.