See:
SE4 Mod archive
SE4 AI/Shipset archive
SE4 Maps/Scenarios archive (LCC seems to have spammed this one instead of appending to his Posts

)
Before you get too entrenched in normal SE4's system, try Pirates&Nomads v2 (see my sig below) It is way out there, and changes the basic propulsion system, as well as giving way more defensive options.
Note on how SE4 deals with mods:
All modded files go into a sub-folder in your SE4 folder.
The mod folder should have a structure very similar to the SE4 folder, with sub-folders called "data", "pictures", "ai", or whatever the mod needs to change.
To activate a mod, edit "path.txt" (found in your SE4 folder), and change the only entry from "none" to the name of the folder containing the mod you wish to play (eg. "piratesmod")
Games saved under one mod may crash or act very strangely when loaded under a different mod. Unless the mods are specifically said to be compatible, don't bother trying to change between them in the middle of a game.
Have fun with SE4!
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The latest info on
Pirates & Nomads (forum thread).
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Download V2.1>- (Now with extra scenario support!)
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Download V1.7>- (With default AIs patched)
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Download compatible EMPs for P&N v1.2 through v1.7>-
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Download SJs latest AI Patcher>-
Visit
My Homepage
Other Links:
-<
Play By Web>-
-<
Schlock Mercenary>- (great space-based webcartoon) -<
First Strip>-
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8-bit Theater>- (fun comic with the pixellated FF1 characters)