Hello.
Tools :
GMax is the tool to make 3D Buildings, Structures and Objects like Cars, Bin, Fences... Those models should be exported usin the FS2004 MakeMDL as scenery objects.
Airport will let you place old fashioned scenery objects, using API models (scasm type code), and create ground polygons, runways... but quite obsolete. However, some functionalities are nice to use in Airport. For example : locating precise lat/lon positions, placing series of objects regularly (Custom RunwayLights) or drawing TaxiwayLines using the Road element... and many more. It's the tool I use in place of FSSC or GroundMaker. The main purpose of Airport is to place objects in scenery.
SceneGenX is the FS9 version of Airport. However, it does not allow you to use th OldFashioned objects or models, and draws elements like Afcad already does. By the way, it usually adds an airport data in its xml type BGL, which overrides your airport when you open it in Afcad. I use SceneGenX only when I want to set Excludes with exact coordinates (using a map, something that is missing in Afcad)
Afcad, you already know will build the path of your aircraft. However, if you do not plan to make custom Ground (Runway, Taxiways, Apron, Grass, Dirt..) Afcad is the tool to make them.
I advice you to use CompileHelper by Arno Gerretsen to compile all your XML and ASM sources. Very usefull as you can place a small shortcut in your source folder, and drag-n-drop the files over..
Easy Object Designer is an old (but very good) tool. Even if all it can do is almost possible to do using newer tools like GMax, there are still some cases where it can be easier to use EOD (RotateToAircraft, IlluminatedGround, Platform...)
LWMViewer is not really a DesignTool, but a Viewer. For example, you can use it to locate the default FS files contening the flattens and VTPGrass around your Airport.
SBuilder can be used to (re-)generate the LWM or VTP polygons you located with LWMViewer. You can build Photoreal textures as well, but personnaly, I think the Microsoft SDK is better for that (the visibility distance is greater)
Some other tools like Rwy12 or ObPlacer are used only to place 3D objects. However, I think that placing objects with simple XML files using a tool like Context for edition is a very good practice.
You will also have the need of the BGLC compiler from the FS2002 SDK to compile your GMAX made GroundPolygons. A bit of knowledge in ASM code is required. You will need MDLCommander or Middleman to "intercept" the MakeMDL dialog box while exporting from GMax. That will allow you to enable the "Keep (source) Files" checkbox. The resulting bgl is useless as your Ground will badly flicker in FS9. You'll have to edit the ASM sources to remove shadows, and replace the ADDOBJ command with an ADDCAT command (with a layer data). And re-copile them using CompileHelper.
If you plan to add some nice features to your airport, such as opening hangars, moving cars - let's call it Animation - GMax is the tool to make them. However, GMax alone is powerless. the CAT tool (very very good tool) can set display conditions for your object.
I would advice you also to read the (entire) Scasm help. There are inside so many old fashioned commands (but still working very well in FS2004). I really think that so many scenery designers are missing a MustHave here. Did I say Pilot Controlled Runway Lights ?
Other tools : ImageTool could be used to quicky view your compressed bitmaps. However, they should be compiled using DxtBmp as it produce better looking textures with less artifacts. I didn't mention the FS2002 and FS2004 Scenery SDKs as it's where I started before understanding that I were going to have the need of other tools. But that was a good practice to learn the how and why..
I'm sorry, I can't tell about FSDS, Instant Scenery, Ground2k4 (as I use SBuilder), FS Architect...
Voilà
Carl