What protocols are safe?
That's easy: none.
The question should be: What protocols are not known to have been broken yet?
The IETF is probably best placed to manage this assuming sufficient funding is around. We also need to improve the funding for public security research and the development (and intelligent review) of open source stacks. What a pity that the spooks don't realise that this makes things safer for everyone: a smidgen of the NSA's or GCHQ's budget would do wonders.