If you use the \mfrac command, from nccmath (medium-sized fraction, ~80% of display style), \smashoperator from mathtools, and the alignedenvironment for the longest rows, it can even all fit on one line.
Note nccmath also has a medsize environment, and a \medop switch.
I replaced eqnarray*, wwhich shouldn't be used anymore, with align*fromamsmath, and the \left[\begn{array} … \end{array}\right] construction with the simpler \begin{bmatrix} … \end{bmatrix}.
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage{fourier, heuristica}
\usepackage[showframe]{geometry}
\usepackage{array, mathtools,bm, nccmath}
\begin{document}
\begin{align*}
\MoveEqLeft
\\
\bm{Fs=}T^{-1}
& \begin{bmatrix}%{c }
\omega _{1}\sum\limits_{i=1}^{T}\hat{u}_{i}+2\hat{u}_{1}\!\!\smashoperator[r]{\sum\limits_{k=1}^{\left(
T-1\right) /2}}\omega _{2k}+2\!\!\sum\limits_{k=1}^{\left( T-1\right) /2}\left(
\sum\limits_{i=1}^{T-1}\hat{u}_{i+1}\cos \left( \mfrac{2ki\pi }{T}\right) \right)
\omega _{2k} \\[3.5ex]
%
\begin{aligned}\omega _{1}\sum_{i=1}^{T}\hat{u}_{i}+2\hat{u}_{1}\!\!\!\smashoperator[r]{\sum\limits_{k=1}^{\left(
T-1\right) /2}}\omega _{2k}\cos \left( \mfrac{2k\pi }{T}\right)
+2\!\!\sum_{k=1}^{\left( T-1\right) /2}\Biggl[ \omega _{2k}\cos \left( \mfrac{2k\pi }{T}\right) & \sum_{i=1}^{T-1}\hat{u}_{i+1}\cos \left( \mfrac{2ki\pi }{T}\right) \\
{} + {} \omega _{2k+1}\sin \left( \mfrac{2k\pi }{T}\right) & \sum_{i=1}^{T-1}%
\hat{u}_{i+1}\sin \left( \mfrac{2ki\pi }{T}\right) \Biggr]
\end{aligned}\\[5ex]
%
\begin{aligned}
\omega _{1}\sum_{i=1}^{T}\hat{u}_{i}+2\hat{u}_{1}\!\!\!\smashoperator[r]{\sum_{k=1}^{\left(
T-1\right) /2}}\omega _{2k}\cos \left( \mfrac{4k\pi }{T}\right)
+2\!\!\sum_{k=1}^{\left( T-1\right) /2}\biggl[ \omega _{2k}\cos \left( \mfrac{%
4k\pi }{T}\right) & \sum_{i=1}^{T-1}\hat{u}_{i+1}\cos \left( \mfrac{2ki\pi }{T}%
\right) \\
{}+{}\omega _{2k+1}\sin \left( \mfrac{4k\pi }{T}\right) & \sum_{i=1}^{T-1}%
\hat{u}_{i+1}\sin \left( \mfrac{2ki\pi }{T}\right) \Biggr] \\
\end{aligned}\\[-2ex]
%
\vdots \\[-1.5ex]
\vdots \\
%
\begin{aligned}
\omega _{1}\sum_{i=1}^{T}\hat{u}_{i}+2\hat{u}_{1}\!\!\!\smashoperator[r]{\sum_{k=1}^{\left(
T-1\right) /2}}\omega _{2k}\cos \left( \mfrac{2k\left( T-1\right) \pi }{T}%
\right) +2\!\!\sum_{k=1}^{\left( T-1\right) /2}\Biggl[ \omega _{2k}\cos \left(
\mfrac{2k\left( T-1\right) \pi }{T}\right) & \sum_{i=1}^{T-1}\hat{u}_{i+1}\cos
\left( \mfrac{2ki\pi }{T}\right) \\
+\omega _{2k+1}\sin \left( \mfrac{2k\left(
T-1\right) \pi }{T}\right) & \sum_{i=1}^{T-1}\hat{u}_{i+1}\sin \left(\mfrac{%
2ki\pi }{T}\right) \Biggr] \\[0.5ex]
\end{aligned}
\end{bmatrix}%
\end{align*}
\vskip 1cm
{\small\begin{align*}
\bm{Fs=}T^{-1}
&\begin{medsize} \begin{bmatrix}%{c }
\displaystyle\omega _{1}\sum_{i=1}^{T}\hat{u}_{i}+2\hat{u}_{1}\smashoperator[r]{\sum_{k=1}^{
\tfrac{T-1}{2}}}\omega _{2k}+2 \smashoperator[l]{\sum_{k=1}^{\tfrac{T-1}{2}}}\left(
\sum\limits_{i=1}^{T-1}\hat{u}_{i+1}\cos \frac{2ki\pi }{T}\right)
\omega _{2k} \\[3ex]
%
\displaystyle\omega _{1}\sum_{i=1}^{T}\hat{u}_{i}+2\hat{u}_{1}\smashoperator{\sum_{k=1}^{
\tfrac{T-1}{2}}}\omega _{2k}\cos \frac{2k\pi }{T}
+2 \smashoperator[l]{\sum_{k=1}^{\tfrac{T-1}{2}}}\left(\omega _{2k}\cos \frac{2k\pi }{T} \sum_{i=1}^{T-1}\hat{u}_{i+1}\cos \frac{2ki\pi }{T} + \omega _{2k+1}\sin \frac{2k\pi }{T} \sum_{i=1}^{T-1}%
\hat{u}_{i+1}\sin \frac{2ki\pi }{T}\right)
\\[3ex]
\displaystyle\omega _{1}\sum_{i=1}^{T}\hat{u}_{i} + 2\hat{u}_{1}\smashoperator{\sum_{k=1}^{\tfrac{T-1}{2}}} \omega_{2k}\cos \mfrac{4k\pi }{T}
+ 2 \smashoperator[l]{\sum_{k=1}^{\tfrac{T-1}{2}}} \left(\omega _{2k}\cos\mfrac{%
4k\pi }{T} \sum_{i=1}^{T-1}\hat{u}_{i+1}\cos \mfrac{2ki\pi }{T}%
+ \omega _{2k+1}\sin \mfrac{4k\pi }{T} \sum_{i=1}^{T-1}%
\hat{u}_{i+1}\sin \mfrac{2ki\pi }{T}\right) \\
\\[-3ex]
%
\vdots \\[-1.5ex]
\vdots \\[-1.5ex]
%
\displaystyle \omega_{1}\sum_{i=1}^{T}\hat{u}_{i}+2\hat{u}_{1}\smashoperator{\sum_{k=1}^{
\tfrac{T-1}{2}}}\omega _{2k}\cos \frac{2k( T-1) \pi }{T}%
+2\smashoperator[l]{\sum_{k=1}^{ \tfrac{T-1}{2}}} \left(\omega _{2k}\cos \frac{2k( T-1) \pi }{T}
\sum_{i=1}^{T-1}\hat{u}_{i+1}\cos \frac{2ki\pi }{T}
+ \omega_{2k+1}\sin \frac{2k( T-1)\pi}{T} \sum_{i=1}^{T-1}\hat{u}_{i+1}\sin \frac{2ki\pi}{T}\right)\rule[-3.5ex]{0pt}{3ex}
\end{bmatrix}%
\end{medsize}
\end{align*}
}
\end{document}

\documentclass, only the necessary packages, and\beginand\end{document}. next, don't leave blank lines in math; they produce errors. finally, don't useeqnarray(looking for link to relevant question). – barbara beeton Feb 22 '16 at 16:04eqnarrayvsalign– barbara beeton Feb 22 '16 at 16:09