HHH was never the top guy, but the question depends on what you mean by "top guy".
If by top guy you mean #1 face, no. HHH was never the #1 face. Came close in 2002, but we all saw how WM 18 ended, and it certainly wasn't in HHH's favor, regardless of whether or not he won the match. If you mean #1 heel then yes. From 2003-2005, he was the top heel in Evolution, but I doubt that anyone considers being the #1 Heel to be the #1 guy.
And if by #1 guy you mean the main attraction, the guy who the company is centered around, then no. Try as he might and try as WWE might with their flashbacks, HHH was never that dude. Never. With or without banging the boss's daughter, he couldn't do it. In his defense, that list of superstars who did it is a very short list indeed (Hogan, Warrior, Savage, Flair, HBK, Bret, Austin, Rock, Brock, Taker, Cena, Batista, in the upcoming years maybe Bryan and Punk and upon reflection, one could argue for Randy Orton, Jeff Hardy or Angle).
And here's a myth buster: the guy in 2000-2002, no matter how hard HHH got that push, was The Rock, period. WM2000 should have ended with Rock on top, and 99% of wrestling fans will agree with that. WM 18 a few years later had Rock taking HHH's shine right from under him. And then there's Backlash 2000, and if you hear how that crowd exploded for The Rock, you knew who the guy was.
As for 2003-2007, that's more tricky, but HHH wasn't the guy. 2003-2004 was still Brock. Now from 2005-2007, Cena and Batista were still getting there feet wet in the headliner department, so while it's easy to point at HHH based off name value, I'd argue it was Taker. Honestly, from the end of Evolution to the DX face turn, did HHH really do anything relevant? Sure he had a good couple of matches with Flair, but he was definitely not the focus of the show. Taker, on the other hand, was still going strong as a full time performer. If anyone was tiding the time over, it was him. Besides, he was a heel at this time. No heel was ever the top guy in WWE except McMahon himself, Punk in the latter half of last year w/ Cena's injury and mid-turn Austin/Rock (and maybe, maybe Orton in the off periods where Cena/Batista was injured)
Furthermore, for those that argue who the guy was during those off periods of Cena/Batista injuries, it still wasn't HHH. Those placeholders really aren't considered top guys, but still, those guys were Orton, Punk and Jeff Hardy. And still I wouldn't call them #1 because of that.
dude the top guy means you are getting TOP BOOKING, it has nothing to do with popularity. Comparing HHH to Orton, Punk, and Jeff hardy is just stupid. Punk and Hardy have never main evented Mania, I honestly can't remember if Orton has. HHH received top booking for a huge portion of his career, especially in 2000 and 2002. Nobody can deny the fact that HHH has been booked as the top guy multiple times in his career and for long periods of time. Saying HHH was never the top guy is almost as dumb as when people were saying Cena wasn't successful.