Wich character coding for source under Windows?

Unless you change it, no encoding is used.  That is, characters are just
treated as 8-bit numbers (as they are in all C programs).  Encodings are
only relevant if you want to display a character (or type at a keyboard),
and in general R assumes that you have set your fonts and keyboard to a 
single consistent encoding (which Petr Pikal had not).

You can reencode on input (See ?connections) and on output where there is
an encoding step (see ?postscript).  So if you have Mac files you can
reencode them on read transparently.  What you can't do is to re-encode
text files on output, mainly because there is no way to mark such files 
are encoded.

I know that R can cope with the different formats regarding carriage return
and/or line feed (the Unix, or Windows, or Mac convention), which is very
nice. However, it is not clear in my mind which character encoding is used:
ASCII, ANSI, other? There is not much differences between ANSI and DOS
encoding for instance, for the first 128 characters. But it is very
different for the rest.

I don't believe there is a single `DOS' encoding, rather a whole series of 
codepages.  And ASCII is a 7-bit encoding.  There are various wide 
encodings out there too.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595