Threat Matrix so far hasn't given me the vibe of "evil government agency". The previous version, The Agency, was great, but you had half the people evil, or maybe just one, the big bald guy, and the rest goodie goodie.
Somebody mentioned 7 Days, that never had the evil agency theme, though it did have mistakes, like the city that went crazy due to a buried mistake and the "mutant" kids from a spill of alien fuel during early testing of the sphere.
Special Unit 2 doesn't count in my opinion as that was basically a few people in Chicago knowing more than anybody else.
24 is filled with evil and good.
Alias is such a friggin mess I mention it only for completeness.
Stargate SG-1 is essentially always good, though they have had a few shows with shadow conspiracy type stuff and those NID guys seem less interested in playing fair than the rest of the government.
I should have paid more attention to Jake 2.0 this week I guess. I did like seeing that Watcher guy from Highlander.
Anybody remember the UPN show, or was it Fox, called Secret Agent Man? The police guy on CSI named Brass was the chief and had 3 agents working for his agency, which may have been the NSA or maybe simply an unnamed "black" operation. Of course, it was a precursor to the hideous She Spies, which sucks eggs, even more so that they removed the geek dude who was the girls boss.