How can I make iconv replace the input file with the converted output?

This isn't working because iconv first creates the output file (since the file already exists, it truncates it), then starts reading its input file (which is now empty). Most programs behave this way.

Create a new, temporary file for the output, then move it into place.

for file in *.php
do
    iconv -f cp1251 -t utf8 -o "$file.new" "$file" &&
    mv -f "$file.new" "$file"
done

If your platform's iconv doesn't have -o, you can use a shell redirection to the same effect.

for file in *.php
do
    iconv -f cp1251 -t utf8 "$file" >"$file.new" &&
    mv -f "$file.new" "$file"
done

Colin Watson's sponge utility (included in Joey Hess's moreutils) automates this:

for file in *.php
do
    iconv -f cp1251 -t utf8 "$file" | sponge "$file"
done

This answer applies not just to iconv but to any filter program. A few special cases are worth mentioning:

• GNU sed and Perl -p have a -i option to replace files in place.
• If your file is extremely large, your filter is only modifying or removing some parts but never adding things (e.g. grep, tr, sed 's/long input text/shorter text/'), and you like living dangerously, you may want to genuinely modify the file in place (the other solutions mentioned here create a new output file and move it into place at the end, so the original data is unchanged if the command is interrupted for any reason).

An alternative is recode, which uses the libiconv library for some conversions. Its behavior is to replace the input file with the output, so this will work:

for file in *.php
do
    recode cp1251..utf8 "$file"
done

As recode accepts multiple input files as parameter, you can spare the for loop:

recode cp1251..utf8 *.php

For now

find . -name '*.php' -exec iconv -f CP1251 -t UTF-8 {} -o {} \;

works like a charm