(Lightweight) backup strategies for a LAMP application stack?

I'm researching some lightweight tools to backup a LAMP stack. The two most imporatant pieces are the

php codebase and
the mysql database.

I can tar/bz2 the code and a mysqldump and restore it on a new server (if the old one crashes) and this is more or less fine.

Anyway, are there more complete solutions to this?

e.g. track and re-install additionally installed pear-packages;
track other packages related to the LAMP stack installed via linux package managers, e.g. APC;
keep mysql and php configurations alongside backups and being able to restore them automatically ...
possibly complete server images, which can be restored without the need to reinstall everything ..

I'm curious about hints, tips, experiences, solutions ..

Solution

The PHP code base should be managed in a version control system such as SVN, Git, etc. Just creating a tar doesn't give you many capabilities that a proper version control system gives you.

The trouble with mysqldump is that you have to lock the tables you are dumping to ensure a consistent snapshot. If this takes a long time, other DB operations might timeout while waiting. We use a wonderful script for snapshotting the running database without excessive locks. It was designed for the Amazon/EC2 environment but the principals apply to any Linux system with the xfs file system.