You could always go with a social character.
Senator Kelly is a villain to the X-Men, one that they can't defeat in combat. In the early Dresden books Marcone is a great "background" villain. In a short story set a few months before Changes, we learn that Marcone builds "I do this if Dresden bursts in and I have to kill him" plans into whatever building is serving as his current HQ - which means he's still serving a villain type role at times.
That has me thinking that almost any old style criminal who knows a bit about magic could make a wonderful background villain - from the Godfather to Tony Soprano.
A Resource base character can complicate the PCs' lives by offering rewards to "crimes" connected to them (let's face it - most PCs see laws as things they shouldn't be caught breaking). Make that person a former Changeling who regrets that he choose "mortal" and is targeting the PCs because they have the powers he lacks and you've got a thorn in their sides that will last for game after game.
A non-flashy caster - someone like Molly - could make a wonderful villain.
But to make a good recurring villain, the PCs have to care about the NPC. Either it's a tragically flawed character or it has struck at someone close to the PCs - there has to be some hook to get the PCs invested.
Here are a few NPCs that you might be able to use. One's a hit man with a code, one was warped and twisted by the pre-teen beauty circuit, one's a drug using creep, and the last is a good time thief/con man who doesn't see what he does as wrong. None of them would work well in a stand up fight against a group of PCs but all of them have hooks you can use to tie them to your game in other ways.
http://www.jimbutcheronline.com/bb/index.php/topic,30354.msg1288932.html#msg1288932 (http://www.jimbutcheronline.com/bb/index.php/topic,30354.msg1288932.html#msg1288932)
http://www.jimbutcheronline.com/bb/index.php/topic,24639.msg1044245.html#msg1044245 (http://www.jimbutcheronline.com/bb/index.php/topic,24639.msg1044245.html#msg1044245)
http://www.jimbutcheronline.com/bb/index.php/topic,24639.msg1044868.html#msg1044868 (http://www.jimbutcheronline.com/bb/index.php/topic,24639.msg1044868.html#msg1044868)
http://www.jimbutcheronline.com/bb/index.php/topic,32803.msg1465917.html#msg1465917 (http://www.jimbutcheronline.com/bb/index.php/topic,32803.msg1465917.html#msg1465917)
Hope this helps!
Richard
All the previous answers are good. I will add another one - make the PCs somehow indebted to the villain. Let even the villain show kindness (albeit for his own manipulative reasons). Some foes are there just for hate but others may be respected. And this brings moral conflict inside of the characters. One example. I'm new to the series but speaking of Red Court vamps, let's rebuild the story of Harry and Bianca a bit for your needs.
First confrontation: As in the canon. Due to PCs' actions Bianca is weakened and kills Rachel.
Second confrontation: The PC loses and ends up taken hostage. While the others search for him and ultimately rush for the rescue, let's Bianca have a serious conversation with her captive. The topic could be something like in the introduction to the rulebook, a little philosophy on mortals having choices and monsters not having them. Make her as inhuman as possible ("Today I killed. I had no choice if I wanted to have a choice now. That's why I'm a monster. I love killing <insert some blooddrinking babble here> etc.) The trick is, make the player think it's a usual I-am-so-evil boasting and then let her just stand up and ... leave. Maybe she sets something in the room aflame for effect but ultimately the character is able to free himself and knows that it was the villain who let him go. At that moment, the rest of the party rushes in and finds the PC confused - something very inhuman, a monster, has just acted ... kindly?
Third confrontation: The PC's girlfriend has theatre tickets and invites the hero. She doesn't arrive, though. Shortly after the play starts Binca shows up and sits down on the empty girlfriend's seat. Make the situation as tense as possible and prolong it accordingly. A theatre play is a lot of time after all and the villain makes evident she is going to view and enjoy it in the presence of the PC. Make her use opera glasses, make he ignore all PC's questions make her make remarks on the actors and the play, short - make the PC know who has upper hand here. After some seemingly endless portion of time the play is over and Bianca invites the PC to a short walk through the night streets. They will have civil conversation. If the PC protests, Bianca says something like: "After yesterday's events you should be at least so civil to let ME pick the topic of our conversation." And again, make it almost unbearable for the player. Let the villain switch the topics in a disturbing way, e.g. let her tell the PC the story of her love to Rachel and then let her ask: "Do you, Mr. XY, have a loved one?" Torture the PC and his player with uncertainty, lack of action, seemingly unnecessary conversation, polite small-talk. And let the vampire be one hell of a monster at the same time. After another portion of some of the most unpleasant time in the PC's entire life Bianca will stop a passing car and get in. The last sentences she says might be as follows: "Remember, Mr. XY, who had the choices today and what choices have been made. Oh, and please, bring some flowers on Rachel's grave sometimes. It's the Main Cemetery, grave number 258. Good night." At the same time as Bianca's car is leaving the PC's girlfriend hops off a bus and calls the PC's name. She's ok, just got arrested and her identity confirmed by the police (make something up - not having a ticket "But I bought one!" and having lost her ID "I had it in my purse, I swear!" works fine). Just make clear that it was Bianca who set up the stage.
Result: The villain hasn't become good - she keeps killing people, she keeps manipulating events and spoiling PCs' actions ... but she saved the PC's butt. Twice. Things got personal but also confusing. The PC knows that the villain is evil but she has also lost a loved one due to direct actions of the PC. And yet, deliberately chose not to retaliate. Of course that it's just one of the machinations of the villain but ... is it still comfortable to think of her as of cannon fodder any more?
These are memorable villains :-)
Chrono: Heh, it's 3 AM here and as I'm lying down with a flu and can't sleep a rather entertaining idea crossed my mind. Let's modify a whole story arc :-)
We already have the introduction and Bianca as recurring villain.
Middle phase: Let her reoccur from time to time but sparingly. The PCs might come across some of her schemes but generally speaking she should be a distant mover, not an imminent foe on the street. On the other hand it might be possible for the PCs to meet her on some occasions on Accorded Neutral Ground (I really do like this idea: http://forum.rpg.net/showthread.php?517766-Dresden-Files-RPG-101-Plot-Ideas&p=15095570#post15095570 - what if one of the PCs shares some cultural tastes with a villain? Wouldn't it be funny to discover that you and your powerful vampire foe both like films by Griffith or Antonioni? I mean, vampires are cultivated monsters, aren't they? Monsters, that is... Don't forget that.) The general idea is that both sides should develop some kind of mutual respect. To some degree, of course, as the vampire war is raging. But you can skip or change this phase, it really doesn't matter much. Develop the story according to your tastes and to the response from your players. Make her as monstrous and villainesque or as trustworthy and respectable as it suits your needs. She might be even willing to cooperate on a rare occasion. (My enemy's enemy is my ... ally. For now. Sort of.) Or not. It's up to you.
Climax: Have Bianca be a part of the climatic events in Changes. She's present to the ritual and is the only one of the Red Courts who tries to avert the imminent disaster. With "No, you ****ing retards!" screaming at the soldiers and Red Court aristocracy, she rushes toward the PCs and tries to prevent them from sacrificing Susan. She fails, of course, but as her hand touches the knife at the moment of casting the spell, she's exempt from the effect. She was efectively co-performing the ritual and such potent magic has its fail-safes (or whatever explanation comes to your mind). So in an instant the Red Court is wiped out from existence ... save for a single vampire whose world has just shattered. She's standing there still, not being able to grasp the situation, her icy eyes filled with horror for the first time. She's alone. Technically a Red Queen now but without her kingdom, stripped off everything. Had she just killed the PC outright a few years ago! But then, she played with him, with his fears, she was the cat and he was a mouse. She let him go, hoping to cripple the future actions of the White Council as one of their wizards was indebted to her "kindness". Now the hunter is the hunted and the mouse has become a sabre-toothed tiger. She's frozen, stricken with panic, for the first time in her long and bloody life she doesn't know what to do.
But the situation is interesting from the PC's point of view, too. What now? The Red Court is history but ... there is one vampire left. Given enough time she would repopulate the Earth with new scions. And the St. Giles' Order doesn't exist either. On the other hand it was this particular vampire a few years ago who, given the opprotunity to kill the PC or destroy his family, refused to do that. The PC remembers the keys to his chains, "forgotten" on the table. And the liberating sound of his girlfriend's voice after that horrible, horrible night at the theatre. And both the doctors' verdict and the verdict of the St. Giles' Order's scholars: "She hasn't been harmed in any way." The PC raises his head and the eyes of the human and the monster meet. Her eyes are not the eyes of a human being ... they are the eyes of a cornered animal...
I think I'm going to use that for my campaign :-)