Ones I've found that aren't on the list.
System_BlocklandEssentials (not that many people have it)
Client_Dueling (not that many people have it anymore)
Client_Mute
Client_TMBI (big one)
Script_ItemRotate (my own mod, I'll fix this :P )
System_StaticMaps
Script_AdminApplications (Me and [GSF]Ghost's mod, I'll tell him to release a quick update fixing this)
Client_OrbShift (another one of Nexus' mods)
Client_CRP
All Support_RaycastingWeapons.cs files, which are in TF2 weapons + Item_KeyCard