Upgrade to glossaries version 4.14 (I've only just uploaded it to CTAN, so you may need to wait a few days before it reaches the TeX distributions). This has a new command \glsenableentrycount which enables two extra fields for each entry: currcount and prevcount. The currcount field keeps track of how many times the entry has been used so far. (By "used", that means how many times \glsunset has been used for that entry, so that means used by the \gls-like commands, but not by other commands, such as \glsadd, \glstext or \glsentrytext. The value is reset to zero by \glsreset.) The prevcount field stores the final value of the currcount field as it was at the end of the previous LaTeX run.
In addition, \glsenableentrycount also enables the commands \cgls, \cglspl, \cGls and \cGlspl which are like \gls, \glspl, \Gls and \Glspl but they test if the value of prevcount is 1. If it is, then they just use commands like \glsentrylong or \glsentryfirst (followed by \glsunset). if it isn't, they behave like their \gls etc counterparts.
So your example can be modified as follows:
% arara: pdflatex
% arara: pdflatex
% arara: makeglossaries
% arara: pdflatex
\documentclass{scrartcl}
\usepackage[xindy,style=long,numberline,savewrites=true,acronym,nomain]{glossaries}
\makeglossaries
\glsenableentrycount % enable \cgls, \cglspl, \cGls, \cGlspl
\newacronym{seqse}{SE}{spin echo}
\newacronym{seqffe}{FFE}{fast field echo}
\newacronym{mri}{MRI}{magnetic resonance imaging}
\begin{document}
\printglossaries
\begin{itemize}
\item Multiple use: \cgls{seqse}, \cgls{seqse}, \cgls{seqse}.
\item Multiple use: \cgls{seqffe}, \cgls{seqffe}.
\item One-time use: \cgls{mri}.
\end{itemize}
\end{document}
(I've added arara directives as a reminder of the document build process, but you can ignore them if you don't use arara.) If \cgls seems like too much typing, remember you can define synonyms. For example:
\let\ac\cgls
\let\acpl\cglspl
\let\Ac\cGls
\let\Acpl\cGlspl
The result looks like:

Notes:
- This method will naturally take longer to build your document (since it requires an extra LaTeX run and has to do more stuff when using an entry).
- This method changes
\newglossaryentry (and therefore \newacronym) into preamble-only commands to ensure the entries are defined before the .aux file is read.
- If you use other commands, such as
\glsadd or \glstext the single-use entry will be added to the list of acronyms.
\glsentrydesc{#2} (\glsentryname{#2})will not add a reference to the glossary. Yet, when using this in the hack of http://tex.stackexchange.com/questions/26238/ignoring-an-acronym-that-is-only-used-once to overwrite\gls{}a note in theauxfile will precede thereby still putting a link to the glossary :/. – bioslime Feb 17 '13 at 09:53