Dracula - Tomb of Dracula v.1-4; Apocalypse vs. Dracula miniseries

Deadpool - two mini-series; Deadpool ongoing #1-69; Cable and Deadpoool; upcoming Deadpool solo ongoing

Mystique - Short-lived series under the Tsunami imprint

Thanos - Thanos Quest miniseries; Thanos ongoing title #1-12

Kingpin - Short-lived series that seems to be non-616-continuity (or at least very hard to fit with continuity).

Rune (Ultraverse) - Ongoing series, plus a mini and several Rune Vs... one-shots.

The Brotherhood - Short-lived ongoing, not the established Brotherhood of (Evil) Mutants

Venom - "Series of mini-series" during the 1990s, stating with Venom: Lethal Protector, and encompassing many more; Hulk vs. Venom 1-shot; Trial of Venom 1-shot; Venom -1 issue; more recently, Venom vs. Carnage miniseries; upcoming Venom: Along Came a Spider origin mini

The Hood - The Hood miniseries

Mephisto - Mephisto Vs... #1-4

Apocalypse - Rise of Apocalypse miniseries

Taskmaster - Taskmaster miniseries

Carnage - Carnage: Mindbomb and Carnage: It's a Wonderful Life one-shots; Venom vs. Carnage miniseries

Magneto - Several minis and one-shots over the years.

Dr. Doom - Back-up strip in Astonishing Tales #1-8; Also the co-star of Super-Villain Team-Up #1-15. Later, received two miniseries and a pair of one-shots in connection with the Heroes Return event and Fantastic Four v.3 #25. More recently, starred in the Books of Doom miniseries. Also, the non-mainstream Doom 2099 series.

Galactus - Super-Villain Classics #1 (later reprinted as Galactus: The Origin), Galactus the Devourer miniseries

Green Goblin (Norman Osborn) - Spider-Man: Revenge of the Green Goblin miniseries; see below also

Norman Osborn, Moonstone (Sofen), Radioactive Man (Chen), Swordsman (von Strucker), and Venom (Gargan) - Thunderbolts #110-present, various one-shots.

Loki - Loki miniseries

Super-Skrull - Annihilation: Super-Skrull miniseries

Ronan the Accuser - Annihilation: Ronan miniseries

Masters of Evil - The original Thunderbolts title may or may not qualify, at least for their first 10 or 12 issues. The Heroes Reborn Masters of Evil received a one-shot at one point.

Doctor Octopus - Spider-Man: Doctor Octopus Year One miniseries (Ock is the actual star despite the title)

Bullseye - Bullseye: Greatest Hits mini and Bullseye vs. Punisher

Underworld - Frank Tieri character created as a villain protagonist who got his own miniseries and a Civil War one-shot

Deadly Foes of Spider-Man and Lethal Foes of Spider-Man - The Sinister Syndicate's members and several other villains

Alyosha Kraven - Spider-Man: Get Kraven miniseries

MODOK - Super-Villain Team-Up: MODOK's Eleven miniseries

Sabretooth - Several miniseries

Juggernaut - Juggernaut one-shot in the 1990s and later the Eighth Day: Juggernaut one-shot

I Heart Marvel: Outlaw Love one-shot - The Answer (Spider-Man villain, not the Dan Jurgens Capt. Amer. foe) and Ruby Thursday