None of these are mine... My apologies to the authors that I didn't cite. (I do know that Monsabert (aka Clovis) is the author of the script mod (#5).
Please feel free to correct this list if some are no longer needed, or if you have a new one to add (especially if your name is Phil...

1. (official) siege fix: http://ageoddl.telechargement.fr/temp/PON.rar
2. (user) casus belli fix:
I think one of the things that should be done is essentially turn off Force Casus Belli for the AI. It just gets abused to hell right now.
It's fairly easy to do it:
quickfix - preventing AI vs. AI wars
Since practically all AI nations tend to declare war on one another there is a quickfix to prevent that. Basically you should stop AI from forging CB so they wouldn't be able to start "unjustified" wars.
Go into your PON\VGN\GameData\Diplomacy folder
search for 40-froge casus-Belli file
open it with notepad
change the diplomat cost to 21
From now on forge CasusBelli will cost 21 diplo. points which is so much, that AI won't ever use it, thus no more Austria against Switzerland wars and such.
3. (user) USA rebels fix (caution- applicability questionable, see posts below):
There are some events related to the path to Civil War raising too much rebel sentiment ( Uncle Tom cabin event is by example raising it by 35....).
Open the US CW events file in the Events directory and paste this:
SelectFaction = $USA
SelectRegion = $Washington
StartEvent = evt_nam_USA_provfix|1|0|evt_txt_USA_UncleTomsCabin 1851|Event-img_USA_UncleTomsCabin1851|$Washington|NULL
Conditions
MinDate = 1851/07/01
MaxDate = 1860/07/01
Actions
SelectFaction = $USA
ChangeLoyaltyFac = $EventTheater_Dixie;40
SelectFaction = $REB
ChangeLoyaltyFac = $EventTheater_Dixie;-40
EndEvent
This event will fire and lower the REb sentiment at the end of your next turn. at last, you will not forced to restart your game.
4. (user) Leaders & Diplomats:
Pride of nations
VGN
Settings
GameLogic.opt
Command and Leaders
IDRDeathBySickness anything but 1
I even set
IDR CommandMaximaRank1 from 1 to 4, some more units a 1 Star General may lead
----
VGN
Game Data
Diplomacy
40-Forge CasusBelli.dpl
Diplomat Cost alter 5 to 21
5. (user) Tahlequah spelling fix:
For on going games, try rather this by copying this event in Option_USA_1850 ( events folder)
SelectFaction = $CHE
SelectFaction = $CHE
StartEvent = evt_nam_Save_capitalname|1|0|NULL|NULL|$Norfolk|NULL
Conditions
MinDate = 1850/01/01
MaxDate = 1919/12/31
Actions
SetCapital = $Tahlequah;10
EndEvent
This event should fix the Cherokee capital name.