[RPG] Reflex Saving Throw when flat-footed (or held, etc)

As you and your group correctly suppose, the silence spell works at its best when cast upon an area or an ally.
No SR applies and no ST is required in this case but the area is stationary or moves with the ally, so the intended target (most probably an enemy caster you're trying to silence) could still move outside of the area and cast his spells.

While there are means to prevent this escape (mostly by grappling or tripping the caster or by readying actions to follow him when he moves) there still is some utility in having a silence area that follows the enemy by itself. Of course, the enemy should be the caster you want to silence, not a random foe.
This is a better tactic for it's harder to avoid and/or does not keep one of your party busy with following or disabling the caster. As such, it's perfectly OK if it's harder to set up. The only drawback is that the enemy could also try to get to your casters and silence them as well.
But that casting method has a reason to exist and yes, it works just like you and your friends said.

Only the target of the spell (the centered creature), if any, is subject to ST and SR

The Barbarian is Flat Footed

Under the initiative rules, the SRD says this (emphasis mine, also in PHB on page 137):

At the start of a battle, before you have had a chance to act (specifically, before your first regular turn in the initiative order), you are flat-footed. You can’t use your Dexterity bonus to AC (if any) while flat-footed. Barbarians and rogues have the uncanny dodge extraordinary ability, which allows them to avoid losing their Dexterity bonus to AC due to being flat-footed.

Nerveskitter says this:

You cast this spell when you and your party roll for initiative. Unlike other immediate actions, you can cast this spell while flat-footed. You enhance the subject's reactions in combat, granting it a +5 bonus on its initiative check for the current encounter. If the subject does not make an initiative check within 1 round, this spell has no effect.

Ferocity says this:

He can enter this state as an immediate action, even when flat-footed at the start of combat, so he may apply the enhanced Dexterity modifier to his initiative check.

Both of these abilities let you act as an immediate action even while flat footed, before your regular turn in the initiative order. Neither are your regular action in the initiative order, as they're letting you act out of turn. Thus, neither of them prevent you from being flat footed just by using them.

They might prevent you from being flat footed by making your initiative high enough that you get to act first in the normal order, of course.