Personally, I feel he stopped being so by "Unthinkable", if not earlier. Frankly "Unthinkable" seemed like a symptom of the character's exhaustion rather than his actual shark jump moment. Is he still the coolest, and if so, why? Try to keep the evidence from within the last, say, fifteen years.
I have always liked Doom. The original origin story in FF Anunal # 2 by Lee and Kirby was great and one of my all time favorites. When the recent version of "Bring on the Bad Guys" came out, I was disappointed that Doom's story was the Byrne version that came out in the eighties. Since Byrne left the FF in 1986, the FF and related characters like Doom have not gotten the treatment that X-Men, Spider-Man, and Avengers titles have gotten over the last twenty years. Being older, I remember very good Doom-related stories from the sixties all the way up to 1985. Villians like Magneto, Bullseye, Green Goblin/Osbourne, Venom (who I never liked), Kingpin, and others who do not come immediately to mind have gotten the bigger spotlight since 1986.