For me 3 raids come to mind and each for specific reasons.
Trial - Only because i had to clear it 4 times / week. It was so much pain for me, that it just doesnt bring best memories, even tho the raid and bosses were not that bad of a design on their own.
Naxx v.2 - Some might find it to be some elitist bitching, but all i can say, as someone who cleared naxx 40 in vanilla, they butchered the old naxx in so many ways its sad. They should have left the naxx 40 where it was and just do something new similar to old naxx, but not butcher old naxx and call it a new raid.
DS - Here the thing i hate is the final 2 fights. The idea that the theme of the xpac (Killing DW) was made in such a bad way that i as player almost felt like i was killing some random mob and not the xpack bad boy is just horrible for me. Thanks to the bad design of spine and madness i never got that feeling "Weeehoo, the big bad boy is down" that other xpack end raids had.
If i had to list them in order would be, naxx v2 - DS, would even leave out trial since it wasnt that bad, only the 4 clear/week part was bad.