Hi Jens, thanks for taking the time to file a bug report. I'm having trouble reproducing this issue. When I install apache2 and php5-cgi and copy a simple php file to /usr/lib/cgi-bin, I don't get any opening of /proc files at all. This is the list I see when cgi is forked (the parent process doesn't open any new files on requests):

[pid 30702] open("/usr/local/lib/tls/x86_64/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/local/lib/tls/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/local/lib/x86_64/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/local/lib/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/tls/x86_64/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/tls/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/x86_64/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/lib/x86_64-linux-gnu/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libz.so.1", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libresolv.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libresolv.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libresolv.so.2", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libdb-5.1.so", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libdb-5.1.so", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/x86_64-linux-gnu/libdb-5.1.so", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libbz2.so.1.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libbz2.so.1.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libbz2.so.1.0", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libpcre.so.3", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libpcre.so.3", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libpcre.so.3", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libm.so.6", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libdl.so.2", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libssl.so.1.0.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libssl.so.1.0.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libssl.so.1.0.0", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libcrypto.so.1.0.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libcrypto.so.1.0.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libcrypto.so.1.0.0", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libxml2.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libxml2.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/x86_64-linux-gnu/libxml2.so.2", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libpthread.so.0", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/etc/localtime", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("./php-cgi-fcgi.ini", O_RDONLY) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/bin/php-cgi-fcgi.ini", O_RDONLY) = -1 ENOENT (No such file or directory)
[pid 30702] open("/etc/php5/cgi/php-cgi-fcgi.ini", O_RDONLY) = -1 ENOENT (No such file or directory)
[pid 30702] open("./php.ini", O_RDONLY) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/bin/php.ini", O_RDONLY) = -1 ENOENT (No such file or directory)
[pid 30702] open("/etc/php5/cgi/php.ini", O_RDONLY) = 3
[pid 30702] open("/etc/php5/cgi/conf.d/fredir.ini", O_RDONLY) = 3
[pid 30702] open("/etc/php5/cgi/conf.d/pdo.ini", O_RDONLY) = 3
[pid 30702] open("/usr/lib/php5/20090626/pdo.so", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/etc/nsswitch.conf", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/usr/local/lib/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/lib/x86_64-linux-gnu/tls/x86_64/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/tls/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/x86_64/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64-linux-gnu/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/x86_64-linux-gnu/tls/x86_64/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/x86_64-linux-gnu/tls/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/x86_64-linux-gnu/x86_64/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/x86_64-linux-gnu/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/tls/x86_64/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/tls/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/x86_64/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/lib/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libnss_db.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/local/lib/libnss_files.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/usr/lib/libnss_files.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
[pid 30702] open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/lib/x86_64-linux-gnu/libnss_files.so.2", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/etc/protocols", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/etc/protocols", O_RDONLY|O_CLOEXEC) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/var/www/cgi-bin/test.php", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3
[pid 30702] open("/dev/urandom", O_RDONLY) = 3

Perhaps your code or the way you have configured PHP and/or Apache is causing this? Perhaps you could attach your configs and a sample of code that causes this.

Anyway, CGI is perhaps the worst way to run PHP as it is extremely inefficient to fork and run a new process every request. If you want per-user PHP I'd suggest using php5-fpm and running one daemon per user.

Marking Incomplete pending response to the question about configs.