Nope, there aren't any programs for creating scenarios (well, not really)... To create a scenario you should use the Cheat menu:
With the cheat menu you can change terrain (e.g. add roads), create units (create a settler in the desired spot and hit "b" to build a city), edit cities (e.g. change their size, add city improvements), change money, change governments etc.
Before you start:
Use the "Start on Premade World" option to use a custom map, you'd probably want to assign starting locations in the map editor. Select the number of civs you want. Think carefully about barbarian activity. If you don't want barbarians, choose "Villages only" and turn of goody huts in the Cheat menu. Be sure to "Customize Rules" to make sure the map is flat (if necessary) etc.
I usually also check "Select Computer Opponents" so I can pick the correct civilizations (the ones I assigned the starting locations to in the map editor). But since you don't have full control over which colors will be at play (if there are less than 7 civs), you might want to always select 7 civs and eliminate them when the game has started.
Be sure to always pick a white civ to start with. That way none of the AI will have founded cities and done other things that might conflict with your plans.
When you're doing all the scenario editing with the Cheat menu, try to change everything in the very first turn! Otherwise the AI will start messing things up. When you need to place cities and units for other civilizations, make sure to change the map view and change the human player through the cheat menu.
While there aren't any scenario editors, there are plenty of helpful utilities that can make things easier:
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CivCity and CivTweak to change the startup parameters and city properties.
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MapCopy to copy map information between maps and savegames.
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Gif Xtractor to edit the graphics in the DLL's (e.g. the king's portraits and spaceship parts).
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MapUtility and
MapEdit to help edit your maps.
... There are probably plenty more, but these are some good ones off the top of my head.
If you have FW (Fantastic Worlds) or MGE (Multiplayer Gold Edition) you also have a bunch of editors at your disposal in the Editor menu, to change graphics, edit rules and add events.
If you don't have those editors, you will have to use a text editor (NotePad or WordPad is fine) to edit the rules and other text files, and use an image editor to edit the graphics (MS Paint could do it, but that's not recommended... better is probably
Paint Shop Pro, although that isn't free, or even more advanced tools like
Photoshop,
Pro Motion,
Poser and
Bryce, but you'd probably only want to think about these if you're a real graphics artist).
Hmmm, I'm pretty sure I forgot something...