I personally feel that it's easier to construct a series of "tiers" than to weigh the palmares of a Sean Kelly against those of (say) an Indurain. So, as I see it:
Top Tier: Merckx (won more of every kind of race than anybody: more Grand Tours than Armstrong, more classics that Van Looy)
Tier 2: Hinault, Coppi (Both hold candles to Merckx in terms of versatility, even if they didn't win as often.)
Tier 3: Armstrong, Anquetil, Indurain, Van Looy, Kelly, De Vlaeminck (Specialists: guys who primarily won one kind of race, but did that very well. I'll admit that Kelly sits a bit oddly here, since he wasn't a specialist: he could seemingly win anything BUT the TDF.)
Not sure what to do with Lemond . . . He had a versatility to match Hinault's, and during his high period of 1983-86 had podiums in an amazing breadth of races, but his actual victories were few. After his comeback he narrowed his focus out of sheer necessity. I think that if he hadn't had his accident, he could have made it onto one of these tiers.
By the way, kudos to the guy who put Philippe Thys on his list. Thys was the first guy to win 3 TDFs, and he did it on either side of World War I (1913, 1914, 1919). Is there any doubt that, but for the war, he would have been the first five-timer . . . or even the first seven-timer?