As Baron points out, Percona’s Xtrabackup tool can be used just like InnoDB Hot Backup.
Many are wondering, “is it good enough?” In fact, I wondered the same thing, and after a few weeks of using and testing Xtrabackup (on machines that have MyISAM and InnoDB tables), I can say:
0) We have not run into any problems with backing up InnoDB tables; on the machines we’ve run it on (RHEL 5.3 and Debian) it has been stable.
1) We were able to use one of the binaries provided by Percona — we did not have to compile anything. Binaries are provided for 64-bit versions of Linux
2) Innobackupex is the script analogous to Innobackup. Basically, this is a wrapper script for Xtrabackup that will copy the non-InnoDB tables.
3) Usually we run InnoDB Hot Backup from a non-privileged user. We had to run Xtrabackup as the mysql user; we think this is because it writes a state file in the datadir, but we did not dig too hard — once we saw that running it from the mysql user worked, we just left it like that.
4) Xtrabackup does not have a –compress option like InnoDB hot backup does. Having the option would be useful, but I believe this option will come soon.
Currently, for clients who want a hot backup solution but do not want to pay for InnoDB Hot Backup, Pythian recommends Xtrabackup.