NOAA. GPS. NTSB. FAA. CDC. NPS. USAF. USCG. NRC. etc.
Plenty more, at least when reasonably well funded. There may be flaws with many, but not all government departments buy $400 hammers, and have employees sitting around doing nothing.
Thus, the friendly, though vastly underpaid and undermanned, staff at Minuteman National Historic Park, counts as well in my book as running very well. Same with most similar places.
Frequently it isn't so much the problem with the government departments themselves, it's how the money is appropriated by Congress, often under pressure from lobbyists who help craft bills. It's not so much the people working there that's the waste. The four biggest costs in the Federal budget are Social Security, Medicare/Medicaid, Defense, and interest on the debt. The departments I list above are teeny tiny by comparison, pennies on your tax dollar, and not that wasteful at all - comparable to the private sector.
Is Medicare/Medicaid wasteful, as a whole? Compared to the private sector? In some ways, definitely (Part D). But let's also keep an eye on the alternatives. You seem to be thinking it should all be cut, all of it. What a nightmare world that would be.
Thus, this cuts both ways. I can also point to plenty of private companies that have been completely run into the ground, and ripped a lot of innocent people off. So can you. Would you want Georgia Pacific in full control over the US forest and national park systems? How about ValuJet/Sabertech in charge of airline safety? Jeffery Skilling heading the NYSE with no SEC oversight? Tyler Hamilton heading up a private version of USADA?