Well, Snowden's secure email got burned and run out of business...
What makes anyone think that "secure crypto" will hide what is truly criminal in endeavor or what any government *suspects* is criminal?
As for what software types or tools aid in such investigations, once again, "Visual Analytics", which I, IIRC, saw as far back as 1999 or 2004. It is a friggin' awesome, cool suite of tools. I like it because of its power and eye-candy-like drag-n-drop query interface, if that is what the visuals were when I stumbled upon the company's web site. I think it was around 99. Between tools or offshoot tools like Visual Analytics and live phone and email tapping, and keyboard and microwave sniffing, those on the shit list will be on it until prosecuted or until they cause a cold trail and fall off the radar because of some sense of integrity in agents who choose NOT to fabricate or enhance incriminating evidence.
I'm not FOR bulk recording, but then again, how can it be put back into the bottle? But, now that more and more people will be wary, those truly up to no good will have to go through a lot of expense to get out of what they are doing, mask it better, or muddy up the auditing process to end up being prosecuted for lesser time in the clink as opposed to multiple lifetiimes behind bars.
Those who are NOT doing anything but are somehow on the shit list/watch list better be satyrists, comedians, protected journalists, or or genuine but harmless nutters, or just some commentator all over the map as to be "unpinnable" (tho not impervious to framing, hahaha). In any case those who are not criminals and not harmful or opportunistic whistleblowers will have to learn to self-moderate. Self-moderation is probably the "fall back contingency" most governments, anyway. Cheaper to cultivate self-censorship than to imprison 20% of the country, warp or crash the economy through "holing" jobs, or killing off companies. These tools used against the crims can make iron-clad positions so that a company can be forced to come clean, change its board of directors, and preserve jobs rather than burn down a whole company if only the Board was corrupt with a few other non-Board officers' complicity.
Well, that is, except when enough of the employees were implicated and the Government fragged the entire company, as happened recently in a rare case.