The bardic performance countersong gets a lot of flack because most folks think it's useful exclusively versus harpies and sirens the like when, in fact,
Countersong Is Actually Pretty Versatile
I've quoted it below so as to make referencing easier.
[A] bard learns to counter magic effects that depend on sound (but not spells that have verbal components.) Each round of the countersong he makes a Perform (keyboard, percussion, wind, string, or sing) skill check.
So the bard takes a standard action to make a Perform (keyboard, percussion, wind, string, or sing) skill check to start the countersong. Then...
Any creature within 30 feet of the bard (including the bard himself) that is affected by a sonic or language-dependent magical attack may use the bard's Perform check result in place of its saving throw if, after the saving throw is rolled, the Perform check result proves to be higher.
Okay, so that's dumb. Whatever. That's never going to happen. The bard is not going to set up a "countersong shield" in case something sonic or language-dependent happens. He can, of course, but those situations are incredibly rare.
If a creature within range of the countersong is already under the effect of a non-instantaneous sonic or language-dependent magical attack, it gains another saving throw against the effect each round it hears the countersong, but it must use the bard's Perform skill check result for the save. Countersong does not work on effects that don't allow saves. Countersong relies on audible components.
This, however, is incredibly useful. Sonic and language-dependent effects are all over the game, and many of the latter are ongoing and send creatures against their compatriots. Being able to give the fighter another saving throw against the spell suggestion, for example, can be life-saver.
"But How Does the Bard Use It?"
The DM may just tell the characters something like, "When the monster says, 'Defend me from harm,' Regdar turns upon the party," and that's a pretty strong indicator that the effect's language-dependent, but if the DM doesn't make it clear the effect's sonic or language-dependent, the bard may have to identify the effect using conventional means (e.g. Knowledge skill checks, Spellcraft skill checks, previous in-character experience with the monster). The bard (and his party!) will really, really want to identify sonic and language-dependent effects without taking actions--if identification takes a standard action and the bard needs to countersong, he can't until his next turn, and that's too long to wait. The bard should try to become an expert on creatures and effects are vulnerable to his countersong performance so he can start the performance right away.
Once the effect is known to be vulnerable to the countersong performance, the bard takes a standard action to start the countersong. On the affected creature's turn, it gets another saving throw, using the bard's Perform skill check result as the saving throw's result. If the result's high enough the creature's saving throw is successful, and it's as if he succeeded on the saving throw initially.