Никаких существенных ошибок я в логах не вижу.

Посмотрите существует ли каталог с  phpMyAdmin здесь:
P:/home/localhost/www/tools/phpmyadmin

Если данного каталога нет - значит phpMyAdmin находится где-то в другом месте, или он не установлен.

Вот ошибки из файла error

[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:131) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: subdomain.test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:108) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: subdomain.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:85) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: localhost:443 (P:/usr/local/apache/conf/vhosts.conf:39) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: You should not use name-based virtual hosts in conjunction with SSL!!
[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:131) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: subdomain.test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:108) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: subdomain.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:85) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: SSL server IP/port conflict: localhost:443 (P:/usr/local/apache/conf/vhosts.conf:39) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:11 2010] [warn] Init: You should not use name-based virtual hosts in conjunction with SSL!!
[Tue Dec 28 18:26:11 2010] [notice] Apache/2.2.4 (Win32) mod_ssl/2.2.4 OpenSSL/0.9.8k PHP/5.3.3 configured -- resuming normal operations
[Tue Dec 28 18:26:11 2010] [notice] Server built: Jan  9 2007 23:17:20
[Tue Dec 28 18:26:11 2010] [notice] Parent: Created child process 3784
[Tue Dec 28 18:26:11 2010] [notice] Disabled use of AcceptEx() WinSock2 API
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:131) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: subdomain.test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:108) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: subdomain.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:85) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: localhost:443 (P:/usr/local/apache/conf/vhosts.conf:39) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: You should not use name-based virtual hosts in conjunction with SSL!!
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:131) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: subdomain.test1.ru:443 (P:/usr/local/apache/conf/vhosts.conf:108) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: subdomain.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:85) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: SSL server IP/port conflict: localhost:443 (P:/usr/local/apache/conf/vhosts.conf:39) vs. Tools.localhost:443 (P:/usr/local/apache/conf/vhosts.conf:154)
[Tue Dec 28 18:26:12 2010] [warn] Init: You should not use name-based virtual hosts in conjunction with SSL!!
[Tue Dec 28 18:26:12 2010] [notice] Child 3784: Child process is running
[Tue Dec 28 18:26:12 2010] [notice] Child 3784: Acquired the start mutex.
[Tue Dec 28 18:26:12 2010] [notice] Child 3784: Starting 25 worker threads.
[Tue Dec 28 18:26:12 2010] [notice] Child 3784: Listening on port 443.
[Tue Dec 28 18:26:12 2010] [notice] Child 3784: Listening on port 8648.
[Tue Dec 28 18:26:12 2010] [notice] Child 3784: Listening on port 443.
[Tue Dec 28 18:26:12 2010] [notice] Child 3784: Listening on port 80.
[Tue Dec 28 18:26:22 2010] [error] [client 127.0.0.1] File does not exist: P:/home/localhost/www/\xd1\x8b\xd1\x84\xd1\x88\xd0\xb5
[Tue Dec 28 18:27:32 2010] [error] [client 127.0.0.1] File does not exist: P:/home/localhost/www/test1
[Tue Dec 28 18:28:51 2010] [error] [client 127.0.0.1] File does not exist: P:/home/test1.ru/www/favicon.ico
[Tue Dec 28 18:28:54 2010] [error] [client 127.0.0.1] File does not exist: P:/home/test1.ru/subdomain/favicon.ico
[Tue Dec 28 18:29:00 2010] [error] [client 127.0.0.2] File does not exist: P:/home/custom/www/favicon.ico
[Tue Dec 28 18:29:00 2010] [error] [client 127.0.0.2] client denied by server configuration: P:/denwer/www/denwer/errors/404.php
[Tue Dec 28 18:29:05 2010] [error] [client 127.0.0.2] File does not exist: P:/home/custom/www/favicon.ico
[Tue Dec 28 18:29:05 2010] [error] [client 127.0.0.2] client denied by server configuration: P:/denwer/www/denwer/errors/404.php
[Tue Dec 28 18:29:14 2010] [error] [client 127.0.0.2] File does not exist: P:/home/custom/www/favicon.ico
[Tue Dec 28 18:29:14 2010] [error] [client 127.0.0.2] client denied by server configuration: P:/denwer/www/denwer/errors/404.php
[Tue Dec 28 18:29:15 2010] [error] [client 127.0.0.2] File does not exist: P:/home/custom/www/favicon.ico
[Tue Dec 28 18:29:15 2010] [error] [client 127.0.0.2] client denied by server configuration: P:/denwer/www/denwer/errors/404.php
[Tue Dec 28 18:31:21 2010] [error] [client 127.0.0.1] File does not exist: P:/home/localhost/www/phpmyadmin
[Tue Dec 28 18:31:46 2010] [error] [client 127.0.0.1] File does not exist: P:/home/localhost/www/sait/tools