Align in Substack

This essentially duplicates \substack, but adding an alignment point.

\documentclass{article}
\usepackage{amsmath}

\makeatletter
\newcommand{\subalign}[1]{%
  \vcenter{%
    \Let@ \restore@math@cr \default@tag
    \baselineskip\fontdimen10 \scriptfont\tw@
    \advance\baselineskip\fontdimen12 \scriptfont\tw@
    \lineskip\thr@@\fontdimen8 \scriptfont\thr@@
    \lineskiplimit\lineskip
    \ialign{\hfil$\m@th\scriptstyle##$&$\m@th\scriptstyle{}##$\hfil\crcr
      #1\crcr
    }%
  }%
}
\makeatother

\begin{document}
\[
\sum_{\substack{n=1\\n\neq i}}^N
\sum_{\subalign{n&=1\\n&\neq i}}^N
\sum_{\subalign{uvw&=1\\n&\neq ijk}}^N
\]
\end{document}

You could define your own specialized array environment, along the lines of the following example; the first expression uses a "regular" \substack expression, and the second uses a custom array environment called mysubarray. (I offer my abject apologies in advance for the lack of mathematical meaning -- the example is merely meant to illustrate the typographic aspects.)

\documentclass{article}
\usepackage{array,amsmath}

\newcolumntype{L}{>{\scriptstyle}l}
\newcolumntype{C}{>{\scriptstyle}c}
\newcolumntype{R}{>{\scriptstyle}r}
\newenvironment{mysubarray}{%
  \scriptstyle
  \setlength\arraycolsep{0pt}%
  \setlength\extrarowheight{-1ex}
  \renewcommand\arraystretch{0}
  \begin{array}{RCL}}{\end{array}}

\begin{document}
\[
\sum_{\substack{xyz=1\\n\neq 45}}^N
\quad\text{vs.}\quad
\sum_{\begin{mysubarray}
      xyz&=&1 \\ n&\neq&45
        \end{mysubarray}}^N
\]
\end{document}

You can also use \mathmakebox from mathtools

\mathmakebox[width][pos]{content}

MWE:

\documentclass{article}
\usepackage{mathtools}
\usepackage{calc}   %% provides \widthof

\begin{document}
\[
\sum_{\substack{xyz=1\\n\neq 45}}^N
\quad\text{vs.}\quad
\sum_{\substack{xyz=1\\\mathmakebox[\widthof{$xyz$}+2\fboxrule][r]{n} \neq 45}}^N
\]
\end{document}