Other than the support with other mods gained through Minecraft Forge, Thermal Expansion integrates with a bunch of mods in particular. This page lists those mods, and how Thermal Expansion integrates with them.
The recipes of most Machines that process items or fluids can be looked up through NEI. Furthermore, Machinist's Workbenches have support for NEI's
? button, which automatically draws recipes onto the crafting grid.
The Fluid Transposer can extract Honey, Fruit Juice and Seed Oil from various items, just like Forestry's Squeezer can.
The recipe lists of most Machines are registered with EE3, so that it can calculate more accurate EMC values with them.
Machines and various tools and materials in the mod are given appropriate Aspects for research or extracting Essentia.