Stock

Stock is the default "mod" for any game; if you don't specifically select a mod, you'll wind up playing stock.

It's generally accepted that as the series has progressed, at least since SE3, stock has grown less and less balanced, and the numbers have grown bigger and bigger. SE5 even has a "balance mod" which was developed by one of the beta testers as a replacement for Aaron Hall's stock files; sadly it wasn't completed in time for release, and instead became an independent mod.

Space Empires I and II
These games did not support mods, unless one counts hex editing!

Space Empires III
SE3 introduced modding to the series. It included a mod editor with which you could edit pieces of the game, such as components. The mod files were binary, so you could not edit them by hand; you had to use the editor.

Space Empires IV
SE4, sadly, eliminated the mod editor. However, it did introduce human-editable mod files.

Space Empires V
SE5 kept the human-editable mod files from SE4. In addition to other new features, it also allowed mods to fall back on stock files, if the modder didn't want to change a particular file. (SE4 had required all mods to contain the full set of files, even if some of them were identical to stock.)