The current best example of this is ACTA, the anti-counterfeiting treaty currently being developed in the deadest secrecy possible (which isn't all that secret) by a variety of major countries. As Ars pointed out this weekend, ACTA is going *way* beyond its theoretical remit -- it's now getting to point of creating its own self-perpetuating secretariat that may well take over control of a lot of world intellectual property management.
As a treaty, ACTA may or may not be fundamentally evil (I'm concerned but not certain); as a process, it's a total fuckup. This is a *very* important treaty, which will govern all sorts of intellectual-property issues in the years to come. But it has been shrouded in secrecy, to the point where the European Parliament has (by a massive non-partisan majority) issued a statement condemning the whole thing and demanding to be let in on the negotiations. (That is, even the Parliament has been kept out of the loop, depending on leaks to find out what's going on.)
I'm really immensely disappointed in the White House over this one. In most cases, I can at least see their side of why they have made the compromises they have, but this one's unforgiveable -- there is no excuse for negotiating something this critical and far-reaching without allowing public commentary. Yes, that makes the process harder -- but major treaties are *supposed* to be difficult, lest they be too casually over-reaching.
(Mind, I don't think there's anything particular to the Obama administration here: most presidents in the past couple of decades have been too fond of secrecy. But transparency has been a specific goal of this administration, and they are absolutely failing in it in this particular respect. Their excuse is that their negotiating partners are demanding the secrecy, but I call bullshit: the US is the 300-pound gorilla of the IP world, and should damned well use its leverage to make this work better.)
Note that I'm not specifically criticizing the treaty itself -- given that I have little better than hearsay to go on, that's hard to do. (Which is my point.) From the rumors, I'd probably give it a C, getting some things right and some things wrong. But the process gets an F...