Feel free to name some. Also name some one-shots if you wish.

Doom
Mephisto
Galactus
Juggernaut
Our Lord Magneto
Sabretooth
Mystique
Zemo
Quicksilver? - I'm unsure. He was kind of villainous in Son of M/Silent War.
Venom

City of Heroes is BACK!

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

Kingpin
Kraven
Vulcan (Emperor Vulcan storyline)
Apocalypse (Rise of Apocalypse)
Dracula (Books of Dracula)
Taskmaster (if I'm noy misaken)
Bullseye (Greatest Hits from the Knights imprint)
The Hand (Elektra: the Hand mini)

The Yellow Claw had his own series.

Because I skipped 90% of Civil War, I missed his one-shot. What was it called? I really enjoyed the first mini-series, and have been hoping for more Underworld appearances(although I could do without the name...)