Individual And Collective Continuing Villains In The Works Of Five Authors

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(i) Ian Fleming.
(ii) Poul Anderson.
(iii) SM Stirling.
(iv) Stieg Larsson.
(v) John Sanders.

(i) Ian Fleming
Fleming presents a new individual villain in each installment and also excels at collective villains. (See More Villains, What To Look Out For and Clandestine Lunarians And Others.) Apart from SMERSH and SPECTRE, several criminal organizations are mentioned or appear more than once, e.g., the Mafia is represented in:

Goldfinger's Hoods' Congress;
Blofeld's SPECTRE;
The Man With The Golden Gun's Group.

(ii) Poul Anderson
Main individual villains:

Aycharaych in the Dominic Flandry series;
Merau Varagan in the Time Patrol series.

Main collective villains:

the Merseians in the Dominic Flandry series;
Neldorians and Exaltationists in the Time Patrol series (but there is a threat even greater than them).

(iii) SM Stirling
Stirling imagines purer evil than anyone else.

An individual villain: the demon-worshiping cannibal, Count Ignatieff.
An evil slave-owning nation: the Draka.
An evil species: the Shadowspawn, the originals of demons and vampires.

(iv) Stieg Larsson
Individual villain: Zala.
Collective villain: the Section, covering up for Zala.

(v) John Sanders
An individual villain: Guido Fawkes, son of Guy Fawkes.
Collective villain: the Sealed Knot.

Since Poul Anderson wrote both historical fiction and science fictional secret service fiction, I recommend Anderson fan's to read John Sanders' long out of print historical secret service series if they can find it. You will certainly appreciate how Sanders boosts the Sealed Knot as a collective villain:

"'...that Cavalier terrorist organization with which I think you are familiar.'
"Pym's smile froze. 'Mr. S.K.,' he breathed. 'I might have guessed the Sealed Knot would be involved in this.'"
-John Sanders, The Hat Of Authority (London, 1966), 2, p. 23.

"'Every assassination attempt upon the Protector, every malicious rumour, every gathering together of traitors, malcontents and rogues of every sort, can be traced directly to the organization of the Sealed Knot. To date, thank God in His mercy, we have foiled them all.'"
-ibid.

The man conversing with Pym is his superior, John Thurloe. According to Thurloe's Wikipedia article, his intelligence service "...broke the Sealed Knot." There is now a historical reenactment society of that name.

Thurloe was a real person. Also Fleming's Head of SMERSH, G., answered to Serov, a real person.

And that is plenty about villains for the time being.