You can use the empheq package and then define your own boxing command. It can be a standard Latex \fbox or a Tikz box, or any other type of box. Look at the example below. I have defined a color box (to make it more interesting) with two optional arguments for padding the space above and below the equation
\mybluebox[<top pad>][<bot pad>]{<contents>}
The keyval package is already loaded so you can make a fancy keyval interface, but I leave that as an exercise to the reader ;-)
\documentclass{article}
\usepackage{color}
\definecolor{myblue}{rgb}{.8, .8, 1}
\usepackage{amsmath}
\usepackage{empheq}
\newlength\mytemplen
\newsavebox\mytempbox
\makeatletter
\newcommand\mybluebox{%
\@ifnextchar[%]
{\@mybluebox}%
{\@mybluebox[0pt]}}
\def\@mybluebox[#1]{%
\@ifnextchar[%]
{\@@mybluebox[#1]}%
{\@@mybluebox[#1][0pt]}}
\def\@@mybluebox[#1][#2]#3{
\sbox\mytempbox{#3}%
\mytemplen\ht\mytempbox
\advance\mytemplen #1\relax
\ht\mytempbox\mytemplen
\mytemplen\dp\mytempbox
\advance\mytemplen #2\relax
\dp\mytempbox\mytemplen
\colorbox{myblue}{\hspace{1em}\usebox{\mytempbox}\hspace{1em}}}
\makeatother
\begin{document}
\begin{empheq}[box={\mybluebox[5pt]}]{equation*}
c_i = \sum_j A_{ij}
\end{empheq}
\begin{empheq}[box={\mybluebox[2pt][2pt]}]{equation*}
c_i = \langle\psi|\phi\rangle
\end{empheq}
\end{document}
