League of Extraordinary Gentlemen and Cowboy Bebop both sound like cool ideas.
I'm busy playing in a campaign at the moment, but I have some ideas for running one.
I don't usually like published adventures, but I have downloaded all of the D20M adventures that WoTC puts on their site. I actually really like the Trouble at Black Rock and No Man's Land adventures and I'm planning on running them for my group. Not only are they good on their own, but I've thought of a way to connect them.
The great thing about both adventures is that, even though they include magic, they can be explained away as technology by a creative DM. This can keep the players guessing as to whether or not they are witnessing magic.
Basically, here's how the adventures would go in my campaign. Right now the campaign would probably lean towards having some very low level magic with ancient alien technology being responsible for most of the things that seem to be magic.
Possible spoilers for the two adventures ahead!
The PCs enter Black Rock, drawn by the mysterious phone calls. Obviously if they are defeated the adventure ends...

If they defeat the machine they should discover a piece of scrap metal on the machine that was used to patch some damage. On this scrap of metal there is a plate with some serial numbers and a name; USS Cyclops. A little research will tell them the ship's history, and the circumstances of its mysterious disappearance. This information will lead them to a man at the local museum who can tell them more. The museum is opening a new exhibit on WWI (No Man's Land). The man that raises the dead bodies in this adventure uses some incantations, and some strange silver-grey powder. This powder matches residue found on the USS Cyclops plate that was used as a patch on the machine from Black Rock. Is there a connection?
The museum curator can give them a list of people (former military personnel and people who investigate strange phenomena) who might be able to help them. Eventually it will be found that the ill-fated ship was seen after its supposed disappearance, pressed into service near Nazi Germany. Its cargo is unidentified ore from Tunguska Russia. After this it vanishes again (the Germans don't even know why).
It resurfaces again, on the shore of one of the Great Lakes of all places, in the year 1999. The ship is immediately confiscated by the US government and its reappearance is hushed up. Soon after, the ship is dismantled. Some parts remain in the custody of government agencies, the rest is destroyed. Not long after a scrap yard sells some metal to a man who wants to repair the used wood chipper he just acquired...
Where will all of this lead? I'm not sure, but taken to its extreme;
Translated from alien language:
Log 133: While examining planet Ter9-A, four subjects escaped the lab and made it to the planet's surface. Searches for them have been fruitless. Adam, his mate and their offspring have vanished. Lilith has gone missing as well, though Sub-Overseer Treag doubts she is with the others. Seekers have been deployed to retrieve them.
The planet is not currently suitable for our needs. Terra-forming may be an option if a ready world is not found in the vicinity.
The loss of these specimens is disappointing, and possibly dangerous. The seekers left behind may have to put them down if the device they have in their possession has been activated.
Seeker K73's Memory File - 011476: Subject Cain employed in elimination of fellow escapees.
Counter - nano-units keeping Cain in thrall state not functioning within normal parameters.
Query - Cain body should only be vessel for nano at present but subject is showing residual persona resonance. Possible for Cain's persona to resurface from death state and usurp nano units' control over body?
Possibility marked at .0000019%.