There are all kinds of organizations that may or may not exist, that have existed in the passage you use. The Knights Templar come to mind immediately. Add to that the Knights of Malta, the Teutonic Knights, the Equestrian Order of the Holy Sepulchre of Jerusalem, and you got the beginning of an interesting conspiracy. What about the Assassins, throw in some Freemasons with their connection to various government officials and agencies in the past, what about J Edgar Hoover? That individual I can easily see being part of an anti-supernatural agenda, and what about scientists.
Science, considering how it acts around magic, could easily be used as a rallying cry for rationality versus magic. Maybe Tesla was this organizations weapons designer and greatest martyr. In fact from this organization's point of view the actions of Kemmler were an attack by the magical community versus the non-magical community. From this organization's point of view Kemmler might be how they view all wizards to be. Also may be the wizards and other supernaturals have corrupted the various governments, controlling the human politicians to further the supernatural creatures goals.
There is all kinds of ways this organization could play out, how do you see it? Racial purity, ideological purity, scientific/rational purity all these or one of these could easily make a starting point for this group.

Just wandered in and saw that you are back and you brought a new DFRPG program with you, now that is how to make an entrance. 

Welcome back and I'll start playing with the program ASAP.

I can think of a decent reason for a warden to be involved: Accusations of lawbreaking, which seems like a great thing for a spurned lover to throw around.

Hmm two wizards split up, relationship ends badly, lots of hurt feelings then a new lover gets killed in a very messy/odd/unusual way. Pretty routine, then have the dead lover be a changeling and now mommy/daddy from the fae side is making nasty noises to White Council.

The Fae ask for and get a representative to 'assist' and 'advise' the Wardens of the White Council in the investigation.

Add to the mix what if the death is non-magical but the Fae still want revenge for the death toss some mortal cops in the mix a few red herrings and give that GM cackle.

Could be fun. Also because of the War, the Wardens are told to wrap it up quickly, i.e. find someone to hang this on and get back to the front lines by various higher ups.

Lots of good ideas:

*Definitely using rosenkurtz somehow (akin to Illuminati perhaps)
*Vatican/Nazi involvement- interesting, my team would probably enjoy that.
*Mundane organizations- R.C.Church, Roman Curia, Italian Mafia, Zog's Cadre (Albania nationalists), Filiberto's Cadre (Italian Royalist Movement), Italian Govt., Rome's Municipal Govt, and some terrorist organization.  Anyone think of more?
*All of Malivotti's ideas- my team will appreciate religious cynicism and intrigue.  I just don't want to overstress Vatican.  I need more Rome-sans-Vatican ideas.

My guess is that about 2 of them will be spellcasters (the Dresden veteran and the perennial D&D mage), 1 were-wolf, 1 Pure Mortal, 1 .  So a diverse bunch- but that'll lend to a more open set of stories.

Ok less Vatican ideas, if one of your players is running a werewolf then there is the tale of Romulus and Remus how they were nursed by a she-wolf maybe something in Rome aids or harms werewolves, or Rome has pact with werewolves.

More Italian thing but check out the House of Savoy, the last kings of Italy, forever exiled from Italy itself, why? Maybe a curse, maybe a prophesy, maybe just politics but what if a member of the House is a supernatural and wants to come back.

One interesting organization that has taken root in Rome is SMOM, Sovereign Military Order of Malta, the Knights of Malta. SMOM is part of the Italian Army as a 'allied' unit. Perhaps the Knights of the Cross are just the most visible, the point of the spear as it will. SMOM, the Knights of Malta are the direct descendants of the Knights Hospitaller, when the Knights Templar were dissolved 1312 the Knights Hospitaller inherited much of Templars holdings and property.

Rome has a modern road around it, almost a perfect circle called Grande Raccordo Anulare, what if it is a magical circle to keep Rome safe, or keep something in? A larger ring road is being planned. Why, is the old circle failing?

The Catacombs of Rome date back to the 200's with Pagans, Jews, and Christians all buried in them, just the place for a necromancer or two.

General things about Rome. VERY BAD TRAFFIC. IIRC there are about 12 taxis for every 10,000 people and only 2 or 3 subway lines, metro and buses are popular but heavily used, the city center of Rome bans cars from 6am to 6pm, other areas due to very active night life have nighttime car bans. Cars are bad, motorbikes are worse, scooters are insane. Forget everything you've ever heard about New York, Boston, Houston, even Paris. Rome is the worse for street size, placement, congestion. People who move to Rome are still afraid to drive after living there for more than 5 years...

With Rome as a setting, there is the Italian Mafia to provide generic thugs also if you want another non-faith power you could create a Millionaire who percieved himself as the 'Prince of Rome' and was actively seeking to gain absolute power over Rome.

The connections between the Mafia and the Church are scary to consider, just off the top of my head, the Vatican Bank scandal with Michele Sindona, Sindona was the point man for the Bank and was laundering the drug money for the Gambino Family through the Vatican Bank, when John Paul I learned of this he started an investigation, but the Pope died of natural causes 33 days into office, do you believe in coincidence? You should also check up Roberto Calvi, The Banco Ambrosiano, P2 Lodge (Masonic Lodge, Shadow Government)

Also the Vatican Bank has been involved money laundering of Nazi and pro Nazi loot from WWII, check out information on 'Independent State of Croatia' from WWII (pay note to 1/3 of the Serb population was to be forced to covert to Catholicism.)
Add to that the Vatican Archives and the Nazi habit of occult studies and looting you begin to wonder just what books does the Vatican have hidden away?

The Vatican Secret Archives have over 50 miles of shelves and is estimated to have in excess of 150,000 items with 35,000 items just in the catalogue!! Oh and there are several other Secret Archives one at least for each branch of the Roman Curia, what is in the Holy Inquisition Archive? The complete works of Kemmler maybe? A true copy the Malleus Maleficarum with information on how to discover and defeat Wizards powers and kill them perhaps...   

Also add Opus Dei to the mix...hehe. Something about guys and gals in holy vestment carrying duffel bags filled with body armour and assault weapons all taking and oath of silence just warms my heart when looking for plots. 

Random thought here about Wizards and tech, what if the Black Ops group has an entromancer on the payroll. Wizards then to blow things up but what if said entromancer was able to make a type of Hexing Ward? A Ward that fights back against the Wizards 'make it go boom' effect.

Heck I'd suspect that there could even be supernatural power like that, ever notice how some devices just start working better the closer they get to a tech?   

Don't forget a way to re-size the window, or to side scroll. I can't see the 1/4 of the window because of the screen resolution I normally have to use.

Maybe place the physical description stuff on it's own tab?   

Oh  and thank you for the program, very nice.

My $0.02.

'There are some things worth killing for'

Regards.