InnoDB, like any other ACID compliant database engine, is required to flush the redo log of a transaction before it is committed. Historically InnoDB used group commit functionality to group multiple such flush requests together to avoid one flush for each commit. With group commit, InnoDB can issue a single write to the log file to effectuate the commit action for multiple user transactions that commit at about the same time, significantly improving throughput.
Group commit in InnoDB worked until MySQL 4.x. With the introduction of support for the distributed transactions and Two Phase Commit (2PC) in MySQL 5.0, group commit functionality inside InnoDB was broken.
Beginning with InnoDB Plugin 1.0.4, the group commit functionality inside InnoDB works with the Two Phase Commit protocol in MySQL. Re-enabling of the group commit functionality fully ensures that the ordering of commit in the MySQL binlog and the InnoDB logfile is the same as it was before. It means it is totally safe to use InnoDB Hot Backup with InnoDB Plugin 1.0.4.
Group commit is transparent to the user and nothing needs to be done by the user to take advantage of this significant performance improvement.