Here are four ways for calculating the square root of a number (with varying precision). However, the result cannot be stored in a counter unless it is an integer.
The calculator package
\documentclass{article}
\usepackage{calculator}
\newcounter{mycount}
\setcounter{mycount}{7}
\begin{document}
\SQUAREROOT{\themycount}{\solution}%
$\sqrt{\themycount}=\solution$
\end{document}
The fp package
\documentclass{article}
\usepackage{fp}
\newcounter{mycount}
\setcounter{mycount}{7}
\begin{document}
\FProot\solution{\themycount}{2}%
\FPround\solution\solution{5}%
$\sqrt{\themycount}=\solution$
\end{document}
The pgf package (thanks to Peter Grill for the reminder)
\documentclass{article}
\usepackage{pgf}
\newcounter{mycount}
\setcounter{mycount}{7}
\begin{document}
\pgfmathsetmacro{\solution}{sqrt(\themycount)}%
$\sqrt{\themycount}=\solution$
\end{document}
The l3fp module of the l3kernel
\documentclass{article}
\usepackage{expl3}
\ExplSyntaxOn
\cs_new_eq:NN \calculate \fp_eval:n
\ExplSyntaxOff
\newcounter{mycount}
\setcounter{mycount}{7}
\begin{document}
$\sqrt{\themycount}=\calculate{round(\themycount^(1/2),5)}$
\end{document}
All of these examples give

Storing the result in a counter requires the result to be an integer. Packages 2-4 have means to round a result which would allow to set a counter afterwards. Here is an example with l3fp:
\documentclass{article}
\usepackage{expl3}
\ExplSyntaxOn
\cs_new_eq:NN \calculate \fp_eval:n
\ExplSyntaxOff
\begin{document}
\newcounter{mycount}
\setcounter{mycount}{7}
\edef\solution{\calculate{round(\value{mycount}^(1/2),0)}}
\setcounter{mycount}{\solution}\themycount
\end{document}
expl3'sl3fpmodule,calculator,fp) but that won't help for storing the results in a counter for the reasons already mentioned. – cgnieder Dec 14 '12 at 17:50\usepackage{pgf}, you can use\pgfmathsetmacro{\squarerootofmynumber}{sqrt(\value{mynumber})}. – Peter Grill Dec 14 '12 at 18:02