I am not too familiar with the pecl install. Looks like it expects to find config.m4 in the top-level directory (?).

In our case, the config.m4 is in the extension/ directory. Can you install it from the extension directory instead?

Try something along these lines:

% cd extension
% /usr/local/php/bin/phpize
% ./configure --with-php-config=/usr/local/php/bin/php-config
% make
% make install

Confirming same bug for SLES10SP2


devel:~ # pecl install xhprof
downloading xhprof-0.9.2.tar ...
Starting to download xhprof-0.9.2.tar (Unknown size)
..........................................................done: 1,506,816 bytes
11 source files, building
running: phpize
Cannot find config.m4.
Make sure that you run '/usr/bin/phpize' in the top level source directory of the module

ERROR: `phpize' failed
devel:~ # phpize
Cannot find config.m4. 
Make sure that you run '/usr/bin/phpize' in the top level source directory of the module

devel:~ #

How about removing the extension/ folder (making its contents 
the root) as this seems like the standard for PECL extensions?

When I try to install xhprof with command
$ sudo pecl install channel://pecl.php.net/xhprof-0.9.2
I got:
downloading xhprof-0.9.2.tgz ...
Starting to download xhprof-0.9.2.tgz (931,660 bytes)
..........................done: 931,660 bytes
11 source files, building
running: phpize
Cannot find config.m4.
Make sure that you run '/usr/bin/phpize' in the top level source directory of the module

ERROR: `phpize' failed

Same problem on php 5.2.12 and pear 1.9.0

Confirmed on Debian 5.0 / PEAR 1.9.1:
----%<----
$ pecl install --force xhprof
WARNING: failed to download pecl.php.net/xhprof within preferred state "stable", will instead download version 0.9.2, stability "beta"
downloading xhprof-0.9.2.tgz ...
Starting to download xhprof-0.9.2.tgz (931,660 bytes)
.........................................................................................................................................................................................done: 931,660 bytes
11 source files, building
running: phpize
Cannot find config.m4.
Make sure that you run '/usr/bin/phpize' in the top level source directory of the module

ERROR: `phpize' failed
----%<----

The problem is, that PEAR cannot handle the extension subdir in the packages archive. You should move the source files and the config.m4 one dir up and edit package.xml accordingly. 

Here is a quick workaround for all that like cleanly installed extensions. Works in Debian Lenny, might work elsewhere:
----%<----
pear update-channels
pecl install --force xhprof
cd /tmp/pear/download/
cp -a xhprof-0.9.2/extension/* xhprof-0.9.2/
sed -i -r -e "s%(<file.*)extension/(.*/>)%\1\2%" package.xml 
tar czf xhprof-0.9.2.tgz package.xml xhprof-0.9.2
pecl install --force xhprof-0.9.2.tgz
----%<----

The above workaround for Debian 5.0 works on Ubuntu Lucid if 
you change to the 
/build/buildd/php5-5.3.2/pear-build-download/ directory 
rather than  /tmp/pear/download

Kannan's workaround works - in a nutshell:

wget http://pecl.php.net/get/xhprof-0.9.2.tgz
tar zxf xhprof-0.9.2.tgz
cd xhprof-0.9.2/extension
phpize
./configure
make
make install


... I have no idea why the package is still broken though.

The package is maintained at http://github.com/facebook/xhprof.  I don't think the maintainers are willing to change the structure just to fit pecl's requirements.

It will probably take an update to the pear/pecl code in order to get this extension built properly.

In which case, should it be included in PECL if it doesn't 
work reliably? I have the same problem on Ubuntu 10.04

wget http://pecl.php.net/get/pecl_http-1.7.1.tgz
tar xf pecl_http-1.7.1.tgz
cd pecl_http-1.7.1
sudo phpize

./configure (if you get a curl error 'sudo apt-get install libcurl4-openssl-dev"

sudo make install
sudo echo ?extension=http.so? >> /etc/php5/cli/php.ini

The pecl installer has been fixed to allow xhprof to be installed with no work 
arounds. First upgrade pear via "pear upgrade pear" and then "pecl install 
channel://pecl.php.net/xhprof-0.9.2".