Try the Dynamic Range Compression feature in the audio tab, its much the same as Perian's . While it does not make the volume louder across the spectrum, it does make the soft sounds louder, much like a "night listening mode" on alot of receivers. This is particularly handy if you find yourself turning the volume down during loud action scenes and back up during softer talking scenes and for environments such as iPod viewing using headphones in noisy environments (maybe on a train or bus or something ).
Having said that, as its done at encoding time, there really is no way to reverse it during playback. As well, the available range is quite sensitive, 1.0 is basically "off" and most acceptable levels would fall around the 1.5 - 2.0 setting. I would strongly suggest doing a few test encodes before doing alot of extensive encodes with it.
Also to note: AC3 passthru (like that found in the AppleTV preset ) does not have this feature as well as doesn't need it. The volume is exactly the same as the AC3 track from your source (hence the "pass thru" part ).
http://trac.handbrake.fr/wiki/DynRangeCompression