In Atom #1, we meet the first recurring villain in the Atom saga; The Plant-Man, aka Jason Woodrue. Although human-appearing he's secretly from another dimension, and has powers over some extraordinarily destructive plants. He attempts to take over the country, but the Atom foils his plot with the help of a pixie-like flower spirit named Maya. The story follows the plot outline that was established in the Showcase issues, with the Atom getting involved to help one of Jean Loring's clients. Woodrue would appear again in the Atom and had a significant role in some Swamp Thing stories much later.
The second story featured something of a surprise; it was the return of the villain from Showcase #34, the first Atom story. The surprise in this case was because the villain (Carl Ballard) was non-costumed and non-superpowered. I can't think of an earlier Silver Age case of a return DC villain having neither of those characteristics, with the obvious exception of Lex Luthor, who's clearly a special case.
In the third issue things really got rolling. The Atom's most durable opponent, Chronos, makes his first appearance, as does the Time Pool, his method of time travel. As I have remarked in the past, DC generally found time travel an irresistabile topic, and each of the DC heroes had his own method.
In the Atom's case, it was Professor Alpheus V. Hyatt's Time Pool, which was basically a magnet at the end of a fishing pole. The Atom goes back to the time of Aladdin, where he plays the part of the genie in the lamp.
Chronos was only one of many clock-related DC villains, but he outlasted most of the others. He commits clock-related crimes with clock-related equipment.