Automattic uses Lightspeed (for PHP), nginx (for static content), and Apache (for media uploads). For WordPress-generated content, all server options are approximately the same speed.
Automattic uses beta versions of APC, and provides a 3-5x performance increase. It’s tied closely to the PHP version, so Automattic recently switched from PHP 4 to PHP 5.
MySQL scales well and is easy enough to use that there’s little reason to consider other DBs for WordPress content. Other applications may have different needs. Note: FriendFeed uses MySQL to store schema-less data. Single-table key lookups in MySQL are faster than getting the data from Memcached.
HyperDB solves DB scaling problems.
User-data backed up every hour, if something changed. Every blog backed up every 12 hours. Dedicated MySQL slaves do LVM snapshots for backups.