At its heart the alignat
environment is built on TeX's \halign
. In that environment you can ignore the formatting specifications for a given column by issuing \omit
. Thus writing
\omit\hfill text \hfill
will give you a centered column of text, since the column specification not only included the left/right alignment but also that the meterial is set as mathematics. It is probably best to create a separate command to provide this construction, which may then be used anywhere in an alignat
, align
or similar enviroment, at the beginning of a cell:

\documentclass{article}
\usepackage{amsmath}
\newcommand{\ditto}{{''}}
\newcommand{\ccol}[1]{\omit\hfill #1\hfill}
\begin{document}
\begin{alignat*}{3}
&E&\quad&\ccol{par}&\quad&\Sigma,\\
&\Psi&&\ccol{\ditto}&&\frac{\epsilon V}{1+4\pi\epsilon F},\\
&\Psi&&\ccol{\ditto}&&\frac{(1+4\pi\epsilon F)^2}{\epsilon}.
\end{alignat*}
\begin{align}
E &= mc^2\\
F &\ccol{is another quantity}\\
G &= u^2 + v^2 - w^2 + x^2 - y^2 + z^2
\end{align}
\end{document}
Sould you wish to span multiple columns the relevant command is \multispan
, e.g. \multispan{3}\hfill text \hfill
will place text spread over three columns and centered.
Alternatively, as Harish Kumar suggests you can use array
or tabular
:

\documentclass{article}
\usepackage{amsmath}
\newcommand{\ditto}{{''}}
\begin{document}
\begin{equation*}
\begin{array}{r@{\quad}c@{\quad}l}
E&\mathrm{par}&\Sigma,\\
\Psi&\mathrm{\ditto}&\displaystyle\frac{\epsilon V}{1+4\pi\epsilon F},\\
\Psi&\mathrm{\ditto}&\displaystyle\frac{(1+4\pi\epsilon F)^2}{\epsilon}.
\end{array}
\end{equation*}
\begin{center}
\begin{tabular}{r@{\quad}c@{\quad}l}
\( E \)&par&\( \Sigma, \)\\
\( \Psi \)&\ditto&\( \displaystyle\frac{\epsilon V}{1+4\pi\epsilon F}, \)\\
\( \Psi \)&\ditto&\( \displaystyle\frac{(1+4\pi\epsilon F)^2}{\epsilon}. \)
\end{tabular}
\end{center}
\end{document}
However, the default line spacing from alignat
is better and you don't need to worry about adjusting the math styles.
the easiest fix is to use your second attempt, but instead of just \phantom{+}
,
surround the plus sign by empty groups to force the correct spacing:
\begin{equation}
\begin{dcases}
\label{eq:115}
{\begin{aligned}
U(x,y,z,t)=\int\frac{x'-x}{r^3}[&\phantom{{}+{}}(x'-x)u(x',y',z',t)\\
&+(y'-y)v(x',y',z',t)\\
&+(z'-z)w(x',y',z',t)]d\omega',
\end{aligned}}\\
V(x,y,z,t)=\ldots\ldots,\quad W(x,y,z,t)=\ldots\ldots
\end{dcases}
\end{equation}
for your first attempt, alignat*
isn't meant to be embedded. instead, alignedat
(defined by mathtools
) is appropriate. but you will still need to add empty groups
around plus signs, in this case, the two that are between the ampersands:
\begin{equation}
\label{eq:115}
\left\{
\begin{aligned}
\begin{alignedat}{2}
&U(x,y,z,t)=\int\frac{x'-x}{r^3}[& &(x'-x)u(x',y',z',t)\\
& &{}+{}&(y'-y)v(x',y',z',t)\\
& &{}+{}&(z'-z)w(x',y',z',t)]d\omega',
\end{alignedat}\\
V(x,y,z,t)=.....,\quad W(x,y,z,t)=..... .
\end{aligned}
\right.
\end{equation}

i'm also not sure why you didn't use cases
, but that's a niggle.
Best Answer
I wouldn't try aligning the inequalities: the formulas are too different from each other. Here's a possibility:
It's necessary to use
{-}
because otherwise the minus sign would be detached from the symbol it refers to.