is it the order your mods are stacked in the mod list?
Almost. The list is in decending date order of the files. It is the order in which your plugins are dated.
The rule is "He who loads last, wins". Say you have two plugins that edit a particular piece of armor. The plugin that edits that piece of armor
last in the load order will have its changes applied to the armor, not the plugin before it.
Mlox and Wrye Mash can show you and allow you to edit your load order by easily redating your plugins.