Secret Wars has lots of great Doom bits, but it’s not a Doctor Doom story as such for a lot of the time.
I guess the obvious place to start is the original Doom stories from the Lee/Kirby Fantastic Four.
After that, the John Byrne story revolving around Doom and Latveria is a pretty good one (I forget exactly which issues it is - a quick Google suggests #246-247).
I know “Unthinkable” from the Waid/Wieringo run has a lot of fans, although it’s been a long time since I read it.
I also liked the Doom story from MM’s Ultimate Fantastic Four run (I think it’s his final three-issue arc, but it pulls together a lot of pieces from his earlier arcs too), and the “Masters of Doom” story from the Millar/Hitch run on the regular FF title is a lot of fun too.