How to increase the spacing between equations in "gather"?

This can be achieved by increasing the length \jot which amsmath uses between lines in multi-line formulas. Either write

\setlength{\jot}{value}

or

\addtolength{\jot}{value}

to increase the spacing. It's very similar to Increase spacing in split environment, since it's the same technique though another environment is meant.

Not sure if this is exactly what you're after, but the mathtools manual mentions, in relation to a new environment it provides, that the distance between lines in gather and other multiline environments is set by a dimension called \jot. By changing this length, e.g. \setlength{\jot}{2ex}, you can set it for the entire document.

Said environment is called spreadlines by the way, and changes this setting locally. This example is copied from the manual:

\documentclass{article}
\usepackage{mathtools} % loads and extends amsmath
\begin{document}    
\begin{spreadlines}{20pt}  
Large spaces between the lines.  
\begin{gather}  
a=b\\  
c=d  
\end{gather}  
\end{spreadlines}  
Back to normal spacing.
\begin{gather}  
a=b\\    
c=d   
\end{gather}

\end{document}

The traditional way (inherited from plain tex) is to do

\openup 2ex
\begin{gather*}
a = b \\
c = d \\
e = f
\end{gather*}

Although it's more traditional to use units of \jot rather than ex.