OK, after talking to Joseph Wright I went ahead and wrote a patch for cmssi, which is the standard math font in beamer. The problem is that this font (computer modern sans serif italics) is designed as a text font, so it doesn't contain any information about positioning of accents. Compare these for before and after patching:

Now the answer (hopefully) is in its final version and ready for use. However, what I'm going to write will only work on Unix type systems. Strangely enough, the patch I initially wrote for 10pt works also great for the other sizes.
Here's what you have to do in order to obtain nicely positioned accents. No change to the actual TeX files is needed, and nothing in the output will change except the accent positions. OK, create some testing directory and run the following script. (If you have root rights on your system, you probably want to replace the updmap command with updmap-sys; thanks, Herbert! Moreover, the map file that gets deleted in the end should probably be stored at some proper location, but I'm not sure where.)
# Create the patch file:
echo '17a18,61
> (LABEL C E)
> (LABEL C H)
> (LABEL C M)
> (LABEL C N)
> (LABEL C Q)
> (LABEL C i)
> (LABEL C j)
> (KRN O 177 R 0.1)
> (STOP)
> (LABEL C J)
> (KRN O 177 R 0.22)
> (STOP)
> (LABEL C e)
> (LABEL C m)
> (LABEL C n)
> (LABEL C r)
> (LABEL C B)
> (LABEL C R)
> (LABEL C S)
> (LABEL C Z)
> (KRN O 177 R 0.08)
> (STOP)
> (LABEL C c)
> (LABEL C q)
> (LABEL C s)
> (LABEL C z)
> (KRN O 177 R 0.06)
> (STOP)
> (LABEL C v)
> (LABEL C x)
> (KRN O 177 R 0.04)
> (STOP)
> (LABEL C h)
> (KRN O 177 R 0.02)
> (STOP)
> (LABEL C l)
> (LABEL C U)
> (KRN O 177 R 0.11)
> (STOP)
> (LABEL C d)
> (LABEL C C)
> (LABEL C G)
> (KRN O 177 R 0.12)
> (STOP)
25a70
> (KRN O 177 R 0.1)
61a107
> (KRN O 177 R 0.04)
62a109
> (KRN O 177 R 0.03)
68a116
> (KRN O 177 R 0.08)
70a119
> (KRN O 177 R 0.04)
77a127
> (KRN O 177 R 0.1)
79a130
> (KRN O 177 R 0.07)
86a138
> (KRN O 177 R 0.08)
87a140
> (KRN O 177 R 0.06)
93a147
> (KRN O 177 R 0.09)
95a150
> (KRN O 177 R 0.06)
103a159
> (KRN O 177 R 0.08)
104a161
> (KRN O 177 R 0.1)
111a169
> (KRN O 177 R 0.05)
112a171
> (KRN O 177 R 0.06)
120a180
> (KRN O 177 R 0.08)
122a183
> (KRN O 177 R 0.07)
124a186
> (KRN O 177 R 0.08)
127a190
> (KRN O 177 R 0.14)
134a198
> (KRN O 177 R 0.05)
140a205
> (KRN O 177 R 0.01)
143a209
> (KRN O 177 R 0.1)' > cmssi.patch
# Patch the font metrics of cmssi8, 9, 10, 12 and 17:
for i in 8 9 10 12 17; do
tftopl $(kpsewhich cmssi$i.tfm) > cmssmi$i.pl
patch cmssmi$i.pl cmssi.patch
pltotf cmssmi$i.pl
done
# Include the patched font in beamerbasefont.sty and define its \skewchar:
cp $(kpsewhich beamerbasefont.sty) newbeamerbasefont.sty
sed '
/{OT1}{cmss}{m}{it}/,/{}/{
s|cmssi|cmssmi|g
s|{}|{\\skewchar\\font=127}|}
' newbeamerbasefont.sty > beamerbasefont.sty
# Make the font metric available to the system:
echo 'cmssmi8 cmssmi8 <cmssi8.pfb
cmssmi9 cmssmi9 <cmssi9.pfb
cmssmi10 cmssmi10 <cmssi10.pfb
cmssmi12 cmssmi12 <cmssi12.pfb
cmssmi17 cmssmi17 <cmssi17.pfb' > cmssmi.map
updmap --enable Map=cmssmi.map
# clean up:
rm cmssi.patch cmssmi{8,9,10,12,17}.pl newbeamerbasefont.sty cmssmi.map
This creates six files: five tfm files named cmssmi<n>.tfm , which contain the patched font metrics, and beamerbasefont.sty, which will be used instead of the original beamerbasefont.sty. (I thought that cmssmi is nice for "computer modern sans serif math italics".) Now you're ready to go and test the following example TeX file. This should go into the same testing directory since the above six files are only available there. Feedback is highly appreciated!
\documentclass{beamer}
\newcommand\test{}
\newcommand\testframe[1]{
\renewcommand\test[1]{{$#1 ##1_{{#1 ##1_{#1 ##1}}}$} }
\begin{frame}{}
\test a
\test b
\test c
\test d
\test e
\test f
\test g
\test h
\test i
\test j
\test k
\test l
\test m
\test n
\test o
\test p
\test q
\test r
\test s
\test t
\test u
\test v
\test w
\test x
\test y
\test z
\test A
\test B
\test C
\test D
\test E
\test F
\test G
\test H
\test I
\test J
\test K
\test L
\test M
\test N
\test O
\test P
\test Q
\test R
\test S
\test T
\test U
\test V
\test W
\test X
\test Y
\test Z
\end{frame}
}
\begin{document}
\renewcommand{\baselinestretch}{1.4}\normalsize
\testframe{\dot}
\testframe{\hat}
\testframe{\tilde}
\testframe{\bar}
\end{document}
beamermaintainers, as proposed by Khaled. – Hendrik Vogt Oct 17 '10 at 07:59sansmathaccent? – Paul Gaborit Sep 09 '12 at 15:48sansmathaccentis found, then it should be loaded automatically. But I just tested it with a freshly updated MikTeX, and it didn't work:-(I didn't actually test it with TeX Live. – Hendrik Vogt Sep 09 '12 at 16:59sansmathaccentdidn't work with a freshly updated TeXLive 2012. – Paul Gaborit Sep 09 '12 at 17:09beamerbasefontand the fixed by Joseph Wright look rather different; I don't know why. – Hendrik Vogt Sep 09 '12 at 17:19beamerdistributing withsansmathaccent? Or should it be installed separately? – Willie Wong Sep 10 '12 at 09:12sansmathaccentis a separate package, but it seems to be included in TeX Live by default. – Hendrik Vogt Sep 10 '12 at 10:39sansmathaccentonly for beamer math fonts with serifs? – begeistzwerst Jan 11 '13 at 12:59\usefonttheme[onlymath]{serif}for my slides. The math accents are then placed just as badly. Right now I use theskewworkaround described below. So I wondered if there also is an easier solution in this case. – begeistzwerst Jan 12 '13 at 14:35\usefonttheme[onlymath]{serif}with my TeX distribution, and all the accents were placed nicely. Perhaps with the recent inclusion of thesansmathaccentpackage, a bug was introduced? – Hendrik Vogt Jan 12 '13 at 15:32