First and foremost:

Gryph. Gryph! GRYPH!!!

http://www.bloomilk.com/Custom/6378/gryph

(Although I have to admit I probably won't be happy with however he's statted, especially if he can deal out damage... which is completely wrong for Gryph--when Miller statted him for the Saga RPG, I don't think he was proficient with even Simple Weapons)

Also from the KotOR comic:

--Camper http://www.bloomilk.com/Custom/7748/camper
--Krynda Draay http://www.bloomilk.com/Custom/6520/krynda-draay
--A new Lucien Draay (or a way to decently and easily buff the current one)
--Other Covenant Jedi (unique or non-unique)
--Young Carth Onasi
--Haazen
--Chantique and the Crucible slavers
--Moomo brothers
--Arkoh Adasca

From other comics:

--Villie http://www.bloomilk.com/Custom/7805/vilmarh-grahrk
--Jahan Cross and his droid
--Kerra Holt http://www.bloomilk.com/Custom/6747/kerra-holt
--Maybe some of the Knight Errant Sith
--Maybe the Bothan agent from the Knight Errant novel
--Moff Trachta
--Gauer, Imperial Assassin
--Tank Sunber
--Arca Jeth http://www.bloomilk.com/Custom/7804/master-arca-jeth
--Morgukai warriors http://www.bloomilk.com/Custom/7723/morgukai-warrior
--Master Tholme http://www.bloomilk.com/Custom/6382/master-tholme
--Alto Stratus http://www.bloomilk.com/Custom/6383/alto-stratus
--By the name of all that his holy: NOTHING from the Dawn of the Jedi series yet--it's too soon!

From the movies:

--Boss Nass! http://www.bloomilk.com/Custom/7783/boss-nass
--Watto http://www.bloomilk.com/Custom/6423/watto
--Chief Chirpa http://www.bloomilk.com/Custom/6421/chief-chirpa

Clone Wars animated series:

--Colonel Krell
--Sugi and her the other bounty hunters
--Some of the Dathomiri (including maybe a Fringe Ventress)
--The Anchorites from Mortis (maybe... they might be too "out there")
--Zygerrian slavers
--Duchess Satine http://www.bloomilk.com/Custom/6528/duchess-satine
--Police Droid http://www.bloomilk.com/Custom/7795/police-droid

Video games:
--Remaining playable characters from KotOR/KotORII: http://www.bloomilk.com/Custom/7752/g0-t0 and http://www.bloomilk.com/Custom/6523/hanharr
--Admiral Forn Dodonna http://www.bloomilk.com/Custom/6518/admiral-forn-dodonna
--Anything from the SWtOR game, such as http://www.bloomilk.com/Custom/7719/x2-c3-imperial-astromech and http://www.bloomilk.com/Custom/6608/sith-juggernaut

Misc/Older sources:

--Gallandro http://www.bloomilk.com/Custom/7791/gallandro
--Rokur Gepta
--Valance http://www.bloomilk.com/Custom/7777/valance
--Montross http://www.bloomilk.com/Custom/7776/montross\

From the books:

Some love the the bad girls!
--Tahiri
--Vestara Khai
--Saba Sebatyne (Do we have her yet? I forget?) http://www.bloomilk.com/Custom/6419/saba-sebatyne
--Daala http://www.bloomilk.com/Custom/6385/admiral-daala
--Ysanne Isard
--Viqi Shesh http://www.bloomilk.com/Custom/7721/viqi-shesh

Something to help non-Sep droids squads: http://www.bloomilk.com/Custom/7769/r2-d2--droid-commander

Something to help non-droid Sep squads: http://www.bloomilk.com/Custom/7722/count-dooku--hologram

New Chewie to help buff Han: http://www.bloomilk.com/Custom/7718/chewbacca--wookiee-first-mate

New Nien Nunb to help buff Lando: http://www.bloomilk.com/Custom/7717/nien-nunb--sullustan-pilot

Cheap pieces like these that can help change movement dynamics:

http://www.bloomilk.com/Custom/6550/wookiee-laborer
http://www.bloomilk.com/Custom/6748/terellian-jango-jumper

Something to help broaden the horizons of the Old Republic, like this: http://www.bloomilk.com/Custom/6517/tarsus-valorum

Also, I second QWEK's r2 commander. Its a really cool reflection of R2 is season 3 of the clone wars. I think its spot on.
http://www.bloomilk.com/Custom/7769/r2-d2--droid-commander

+1
Here's my take on him
Jorj Car'das
40, hp 80, def 17, ATk 10, dmg 10
SA
Unique
Double attack
Relay orders
Gather information (replaces attacks; sight, choose one enemy within line of sight, allied characters within 6 squares get programmed target against this enemy for the remainder of the round)
Force 3
Force Teleport (force 3, replaces turn; touch, move one adjacent character to any empty legal square, that character counts as activated this turn. This move does not provoke attacks of opportunity.)
CE
Allied Unique Commanders gain Relay Orders


As well +1 to these of Gweks:
the R2 clone wars model
Republic comit characters tholme, vilie
Agent Cross and his droid
Kerra Holt
Dutchess Satine

Viqi Shesh, though would prefer something like

Viqi Shesh
16, hp 50, def 15, ATk 8, dmg 10
SA
Unique
Diplomat
Peace Brigade
Yuuzhan Vong collaborator 
Relay Orders
Tizo worm(this character counts as yuuzhan vong for the purpose of commander effects)
CE
Peace brigade allies gain Tizo worm and internal strife



And finally two of my own after watching clone wars massacre episode:

Mother Talzin (RM nightsister sith witch)
40, hp 100, def 19, ATk 0, dmg 0
SA
Unique
Nightsister
Melee Attack
Stable Footed
Force 2
Force Renewal 2
Force Lightning 5
Force Shields
Force Conceal (Force 4; replaces turn; touch, adjacent nightsister character with a force rating has invisibility for the rest of the skirmish)
Surprise Move
CE
Allied nightsisters gain synergy +2 and +2 for allied nightsisters


Asajj Ventress, Nightsister (RM Asajj Ventress)
58, hp 130, def 19, Atk 12, dmg 20
SA
Unique
Nightsister
ninman style mastery
melee attack
twin attack
Double Attack
Rival (Cannot be in a squad with a character named Dooku, Tyranous, or Grievous)
Force 5
Master of the Force 2
Force Pull (Force 1, replaces turn: range 6; move target Large or smaller enemy adjacent to this character. Make an immediate attack against that enemy)
Force Leap
Lightsaber Defense

I'd like to see a Han Solo, Covert Operations Leader. Use the Rebel Hero mini but let him hand out Super Stealth/Cloak to all Rebels (&NR if he has affinity) characters with Stealth. This lets the non-commando rebels get in on the SS action. He could also have Disruptive because that's what he does on covert missions. I also wonder if he couldn't give another unique Stealth via a special ability similiar to Nom's.

Imperial Scanning Crew Member
Dexter Jettster
Chief Chirpa
Owen Lars
Beru Lars
Shmi Skywalker
Young Anakin
Sebulba
Coleman Trebor

Defiantly a new ability for the Vong called

Coral Growth: Whenever this character defeats an adjacent living enemy, you can immediately add a character named Yuuzhan Vong Worker to your squad. The new character sets up in a square that enemy formerly occupied.

This is to reflect the coral growth that the vong use on other life forms to keep them as slaves to do work for them.
Im not sure weather or not the workers are designed to reflect the slaves, or an actual worker, but I think it would be a really cool ability.

A new anakin Solo with the force ability Force (Or Battle) Meld, in the books him and 17 other jedi are attacking avong ship and in order to get a one up on them they 'link up' in the force to share thoughts, strategy, and even pain. Its a pretty powerful ability so I think it would make a new good force power and would work something like this. As it is right now the ability would be great for use of many of the lower point generic jedi and have a new form of squad to run.

Battle Meld
Force 3 replaces arracks; For the rest of the skirmish, this character gains the following commander effect (or Special ability): Followers with a force rating get +1 Attack and +1 Defense for each other allied character with a force rating with in 6 squares

I made this: http://www.bloomilk.com/Custom/7543/chewbacca--wookie-life-debt

Yes +1, great idea, with droid reinforcements 10 ( just in case someone brings wuher) from any faction
Maybe:

Watto
Cost18 hp30 def13, atk7, dmg10
SA
unique
flight
strong-willed
gambler's luck
repair 10
Droid Reinforcements 10 (after seeing your opponents squad you may bring up to 10 points of non unique Droid characters into your squad from any faction)

Also some imperial ones:

Nk1 necrosis (RM Grievous JH)
35, hp 80, def 18, atk 12, Dmg 20
droid
stealth
double attack
melee attack
mobile attack
Twin blaster 20
parry
evade

Kueller (RM imperial sentinel)
41, hp 100, def 19, atk 13, dmg 20
SA
Unique
melee attack
double attack
doctrine of fear
Detonator (replaces attacks; one ally within line of sight with self destruct is immediately defeated)
Droid reinforcements 20
Rapport 2 for Death Star Droid 
Force 4
Force Heal 20
Lightsaber deflect
CE
Droids are subject to this effect
Droid characters in your squad gain self destruct 10

Brakiss
20, hp 90, def 18, ATk 11, dmg 20
SA
Unique
melee attack
double attack
betrayal
Dark Tutor (At the start of the skirmish, choose an ally. If that ally does not have a Force rating, it gains Force 1 and Sith Rage and can spend this Force point normally; it is considered to have a Force rating for the rest of the skirmish. If that ally already has a Force rating, it gains 1 Force point.)
Force 4
Force lightning 2, (30 damage within 6 and two characters adjacent to target)
Lightsaber Block
CE
Characters in your squad with a force rating start with an additional force point

Palpatine Reborn
59, hp 130, def 21, ATk 16, dmg 20
SA
Unique
Melee Attack
Double Attack
Betrayal
Corrupted (when this character activates, deal 20 damage to it)
Turn to the Dark Side
Affinity (a follower whose name contains Luke Skywalker Jedi may be in your squad regardless of faction. This character gains internal strife and force ascetic)
Rapport Imperial Sentinels cost 10 less when in the same squad as this character 
Force 2
Force Renewal 2
Master of the Force 2
Transfer Essence
Sith Rage 2
Force Storm
Force Possession (force 3, when this character is defeated, immediately defeat one living enemy character within 6 squares, save 11 If that character is defeated, place this character with full hit points in the space of the defeated character)

What about a Jabba's palace mini set (Like the bar scene and the battle for theed)? New Jabba, leia boushe with Aggressive Negotiations, landos with Spy, maybe even a new boba with Oblivious?