So far I know of the following, separated by weapon type.

Definitive
Bastard Swords:
1) Kondar
2) The Sword of Balduran
3) Albruin (EE)

Daggers
1) Werebane

Longswords:
1) The Burning Earth/Flametongue


Questionable
Quarterstaves:
1) Aule's Staff
2) Staff of Striking

Two-Handed Swords:
1) The World's Edge/+3 Two-Handed Sword

Will the "Questionable" weapons definitely overcome what damage reduction and/or regeneration they have, or will the only 5 definitive weapons work? Also, do any weapons that can obtained and kept legitimately (IE: Not Drizzt's scimitars) also work?

ime the single best way to kill them is with a few traps

Wouldn't likely happen since I have Imoen as a Thief and her points have pretty much gone into Find/Disarm Traps, Open Lock, and Pick Pockets. I just never got the hang of using traps in this series.

So here is my party:
Main character (Cavalier)
Khalid
Minsc
Jaheira
Imoen
Dynaheir

None of the warriors are proficient with Bastard Swords because I forgot about 1) needing them for Werewolf Island until recently (it's been 20 years since I played the game) and 2) forgetting that different proficiencies are needed in the Enhanced Edition of BG1 compared to the original edition. What concerns me is how badly being non-proficient in weapons affects attack rolls (if not damage rolls as well). =/

I think non-proficiency gives a -4 To Hit penalty, and that's all. No damage penalty.

Some googling around to try and confirm it left me with a reference to -4, and a different table saying it is -2 for warrior type classes.

According to Wiki:Weapon Proficiency, Bookwyrm627 is correct that there is no damage penalty. The THAC0 penalty varies by class: 2 for Warriors and Monks, 3 for Priests and Rogues, 5 for Wizards, Mage/Thieves, and Shadowdancers. If I recall correctly, in the Enhanced Edition, equipping a non-proficient weapon will report in the inventory screen the modifier you incur for your lack of proficiency. Therefore, you should pick up a Bastard Sword (any regular one will do), equip it, and check what the inventory screen reports for your chosen character's THAC0 with that sword. You can manually adjust that THAC0 for the bonus that an enchanted Bastard Sword will confer.

The reference to a penalty of 4 might be because a character who dual-wields, while having no proficiency in Two Weapon Style, takes a +4 THAC0 penalty to the main hand (and +8 to the off-hand). If you aren't dual-wielding, then this won't matter to you.

As a general note, I encourage you to check the Wiki if you aren't concerned about spoilers. Every answer I've provided in this thread has been from the Wiki, though cross-checked with personal experience. I don't mind posting answers from the Wiki, but you might get faster results if you checked it yourself. :)

So, as I've mentioned, I have my Cavalier, Khalid and Minsc as my warriors who could possibly wield a Bastard Sword. If they were to try to wield Kondar or the Sword of Balduran without being proficient, would they have much luck hitting them or am I essentially screwed?

as Khalid is a fighter his chance to hit will be better

Cavalier is a Paladin kit. Khalid is a Fighter, no kit. Minsc is a Ranger, no kit. According to Wiki: Classes, Fighters, Rangers, Paladins (and Barbarians - not relevant here) are all in the Warrior group.

Building on my prior post, Wiki: Weapon Proficiency tells us that Warriors get a 2 point THAC0 penalty for non-proficient wielding, so all 3 of those characters will face the same 2 point penalty. Character THAC0 improves with levels. Based on your other thread, all your characters are at least level 7, with some level 8s. For simplicity, I will assume all three warriors are level 7.

According to Wiki: Fighter, a level 7 fighter will have a bare-handed THAC0 of 14. Khalid has only 15 Strength, so he will not get a THAC0 bonus from that. Minsc has 18/93 Strength, so he will get a THAC0 +2 bonus from that. I do not see in either thread a statement of your Cavalier's Strength. You can look up his THAC0 bonus from the Wiki article on Strength.

Kondar gives THAC0 +3 against lycanthropes.
Sword of Balduran gives THAC0 +4 against lycanthropes.

Wiki: Greater Wolfwere says they have AC 2.

Suppose we give Minsc the Sword of Balduran. As a level 7 Ranger, he would have a THAC0 of 14. Due to his Strength, that improves to 12. Using Sword of Balduran against a lycanthrope improves it to 8. His lack of proficiency degrades it back to 10. Thus, he will hit an AC 0 lycanthrope half the time. Since Greater Wolfwere has an AC of 2, Minsc must roll (10 - 2) = 8 or better. Is that hit rate "essentially screwed", or "much luck"?

For all of your Warriors, reaching character level 8 will improve THAC0 by 1.

You have likely been finding various potions of Giant Strength. Using one of these will temporarily improve your warrior's strength. Higher strength values will improve your THAC0. A Potion of Fire Giant Strength would give you 10 turns (100 rounds) of Strength: 22. This would confer a THAC0 bonus of +4. You could give Kondar to Khalid or your Cavalier, then drink a Potion of Fire Giant Strength to obtain a THAC0 even better than Minsc with the Sword of Balduran.

Okay, so in short, I should be fine? That's a lot of gobbledygook to digest, in part because 2nd Edition D&D isn't my strong suit. If we're talking 3.5 Edition, and far less text, then I could follow you easily. =/

I showed my work so that you wouldn't need to rely on a specific conclusion from me, and could tweak the numbers up or down with other equipment, such as Legacy of the Masters. I didn't realize you wanted a simple yes/no answer without an explanation.

Per above, with the setup I proposed, Minsc must roll 8 or better on a 1d20. Therefore, he has a 13/20 = 65% chance of hitting a Greater Wolfwere. If you give him other equipment to improve his THAC0, or have someone use a potion of Giant Strength to improve THAC0, your results get even more favorable. For comparison, with the setup proposed above, but giving Minsc 1 point in proficiency (which you didn't do, but wish you did), would give Minsc a 15/20 = 75% chance of hitting a Greater Wolfwere.

Just before the fight, have Jaheira cast a Bless spell (1st level) for an extra boost To Hit for your fighter types. Looks like she can also use Strength of One (3rd level) to set the strength of multiple party members to 18/75 for 10 rounds if you don't want to use potions, or if you want to boost multiple fighter types and use all the anti-werewolf weapons you have available.

You aren't screwed, just look for which weapons work and check your spell lists for buffs that can help you hit if you need them.

On further inspection of my main character in particular, I came to realize a few of his proficiencies were taken in poor taste, namely the one point in War hammer and two in Sword and Shield Style. The latter only seemed to be worthwhile for Chapter 3, and that's it. I'm tempted to try EE Keeper to fix that but am having trouble making that work. =/

Sadly, I'm not familiar with the game editors, so someone else will have to chime in.

As far as the style proficiencies, I'd suggest just picking one based on whatever you plan to do. I actually took One Handed (whatever it is called) on my Swashbuckler (even though he could get 3 pips in dual wielding) simply so I didn't have to keep going into inventory to swap weapons when I wanted him to use a bow. EE might let you have a bow on swap without having to manually remove the off-hand weapon each time; I don't know.