None of this silence stuff has been much of a problem in my campaign. The PC sorcerer took silent spell and still spell as his first two feats. Got himself out of some nasty pickles too.
But in all editions, Silence has been a potent spell. It's nothing new for 3E/3.5. And there was only one spell that countered it directly then, Vocalize, and it didn't appear until Unearthed Arcana. So, in some ways, 3E was ahead of the curve set by 1st edition in dealing with the spell because at least they had a metamagic feat that could counter it.
I think it would be worthwhile for each spell-casting class to have a spell on their lists as a counter for it, one with only somatic components. If you prepare for being silenced and prep the spell, you're in good shape. If not, you'll learn from your mistakes.
Then again, silent dispel magic spells aren't that far out of reach. And the existance of silence without many other counters makes those metamagic rods of silence spell VERY attractive as a defense. So, even now it's not like there's nothing that can be done.