You can use all of PlainTeX math and most of AMSmath in ConTeXt; for the latter you may need the nath module (see on CTAN).
The "native" ConTeXt way of math is MathML - rather verbose but mighty. Here's the docs:
- MathML (general) by Pragma
- MathML in ConTeXt (examples) by Pragma
- ChemML (MathML extension for chemistry) (screen) by Pragma
- PhysML (MathML extension for physics) (screen) by Pragma
- Steps (XML step charts) (screen) by Pragma
- Euler in ConTeXt (using Euler math font) by Adam Lindsay
Esp. for physics there's the units module.
There's a module for chemical structure formulae: PPCHTeX (works also with LaTeX). It's based on Metapost and MetaFun.
It is also possible to use most LaTeX equations in ConTeXt with a relatively small set of supporting definitions; that is discussed in the LaTeX Math in ConTeXt page.