If you're interested in duplicating the behaviour of \boxed when it comes to the appearance, but remove the height-associated addition (supplied by \fboxrule and \fboxsep), you could define your own boxing macro based on \boxed. This is what \boxed is defined as in amsmath:
\newcommand{\boxed}[1]{\fbox{\m@th$\displaystyle#1$}}
As such, defining \myboxed to be
\newcommand{\myboxed}[1]{%
\rlap{\hspace*{\dimexpr\fboxrule+\fboxsep\relax}%
\phantom{\m@th$\displaystyle#1$}}%
\smash{\boxed{#1}}}
would achieve this. Here is an MWE showing the resulting output for two paragraphs; the first uses \boxed, while the second uses \myboxed:

\documentclass{article}
\usepackage{amsmath}% http://ctan.org/pkg/amsmath
\makeatletter
\newcommand{\myboxed}[1]{%
\rlap{\hspace*{\dimexpr\fboxrule+\fboxsep\relax}%
\phantom{\m@th$\displaystyle#1$}}%
\smash{\boxed{#1}}}
\makeatother
\begin{document}
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Lorem ipsum dolor sit amet,
consectetur adipiscing elit. Aliquam ligula dui, blandit et posuere eu, varius in erat.
Nunc ornare tellus in dui \boxed{3.299\times 10^{29}} tempus facilisis. Nunc ornare tellus
in dui tempus facilisis. \boxed{3.299} Nulla vel dolor augue. Nulla commodo nulla et tortor
aliquam nec lacinia odio sagittis. Aenean vitae interdum dui. Lorem ipsum dolor sit amet,
consectetur adipiscing elit. $3.299\times 10^{29}$ Aliquam ligula dui, blandit et posuere
eu, varius in erat. Nunc ornare tellus in dui tempus facilisis.
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Lorem ipsum dolor sit amet,
consectetur adipiscing elit. Aliquam ligula dui, blandit et posuere eu, varius in erat.
Nunc ornare tellus in dui \myboxed{3.299\times 10^{29}} tempus facilisis. Nunc ornare
tellus in dui tempus facilisis. \myboxed{3.299} Nulla vel dolor augue. Nulla commodo nulla
et tortor aliquam nec lacinia odio sagittis. Aenean vitae interdum dui. Lorem ipsum dolor
sit amet, consectetur adipiscing elit. $3.299\times 10^{29}$ Aliquam ligula dui, blandit et
posuere eu, varius in erat. Nunc ornare tellus in dui tempus facilisis.
\end{document}
You'll note that it also highlights some of the problems with removing the vertical boxing adjustment. @Boris' suggestion to reduce \fboxsep would help. You could also print something more subtle like a shaded box and remove the solid rule. Here's an alternative to \myboxed that achieves that:

\documentclass{article}
\usepackage{amsmath}% http://ctan.org/pkg/amsmath
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
\makeatletter
\newcommand{\myboxed}[2][black!5]{%
\setlength{\fboxrule}{0pt} \setlength{\fboxsep}{1pt}%
\rlap{\hspace*{\fboxsep}%
\phantom{\m@th$\displaystyle#2$}}%
\smash{\colorbox{#1}{\m@th$\displaystyle#2$}}}
\makeatother
\begin{document}
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Lorem ipsum dolor sit amet,
consectetur adipiscing elit. Aliquam ligula dui, blandit et posuere eu, varius in erat.
Nunc ornare tellus in dui \boxed{3.299\times 10^{29}} tempus facilisis. Nunc ornare tellus
in dui tempus facilisis. \boxed{3.299} Nulla vel dolor augue. Nulla commodo nulla et tortor
aliquam nec lacinia odio sagittis. Aenean vitae interdum dui. Lorem ipsum dolor sit amet,
consectetur adipiscing elit. $3.299\times 10^{29}$ Aliquam ligula dui, blandit et posuere
eu, varius in erat. Nunc ornare tellus in dui tempus facilisis.
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Lorem ipsum dolor sit amet,
consectetur adipiscing elit. Aliquam ligula dui, blandit et posuere eu, varius in erat.
Nunc ornare tellus in dui \myboxed{3.299\times 10^{29}} tempus facilisis. Nunc ornare
tellus in dui tempus facilisis. \myboxed{3.299} Nulla vel dolor augue. Nulla commodo nulla
et tortor aliquam nec lacinia odio sagittis. Aenean vitae interdum dui. Lorem ipsum dolor
sit amet, consectetur adipiscing elit. $3.299\times 10^{29}$ Aliquam ligula dui, blandit et
posuere eu, varius in erat. Nunc ornare tellus in dui tempus facilisis.
\end{document}
\myboxed has been fitted with an optional argument to modify the colour (default is black!5 or 5% black):
\myboxed[<colour>]{<stuff>}
\myboxed{...}instead of\boxed{...}where\newcommand{\myboxed}[1]{\smash{\boxed{#1}}}, then you can decide whether a removal of the boxing height works for you or not.\smashputs its contents in a box of height zero. – Werner Nov 17 '11 at 21:34