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Since I found out how to do this, and I know a few others want to know how I will write out this little guide for it.

The code for the augmentation effect is: LineageEffect.w_vari_b2_000_a
The b in b2 stands for blue, this can either be b or r [for red]
The number 2 can either be 1, 2, 3, or 4.  They are slightly different animations.
the following number states what weapon glow it is.
000 = 2 handed sword
001 = Fists
002 = Dagger
003 = Bow
004 = Sword
005 = Blunt
006 = Sword
007 = Polearm / Staff
008 = Bow

So for example, say you wanted a blue effect, with the final animation,  for a sword.  You would use LineageEffect.w_vari_b4_004_a

Now, to add it to a weapon, take a look at a weapon line from weapongrp.dat:
Code:

0	6591	1	1	7	10	0	LineageWeapons.angel_slayer_m00_wp			LineageWeaponsTex.angel_slayer_t00_wp			icon.weapon_angel_slayer_i01					-1	950	47	1	0	7	1	1	LineageWeapons.angel_slayer_m00_wp		1	LineageWeaponsTex.angel_slayer_t00_wp			4	ItemSound.dagger_6	ItemSound.sword_small_2	ItemSound.sword_mid_2	ItemSound.public_sword_shing_7	ItemSound.itemdrop_dagger	ItemSound.itemequip_dagger		5	246	132	3	5	12	-3	0	0	0	433	0	1	1	1000	0	-1	0	LineageEffect.c_u004		0.000000	0.000000	0.000000	0.600000	0.100000						LineageWeapons.rangesample		1.100000	0.700000	0.700000	7.000000	0.000000	0.000000							4	-1	-1	-1	icon.weapon_angel_slayer_i01			

Find this part of the code:
Code:

0	LineageEffect.c_u004		0.000000	0.000000	0.000000	0.600000	0.100000

Change the LineageEffect.c_u004 to LineageEffect.w_vari_r4_004_a
Note : Make sure there is 1 tab before that code, and 2 after or else you will cause an error.

The 5 numbers after that define a few things.
1st number = position on the weapon [how close to the handle, or tip of the blade.
2nd number = vertical position relative to you [so it will move off the blade up or down]
3rd = horizontal position relative to you [so it will move off the blade side ways.]
4th = is how "fat" it will be.
5th = how long it will be.

So just tweek those till you get what you like.  You can even add the effect to weapons below A grade, just be careful about those tabs.

Also, just like the flame effect, how intense this is depends on the opacity command in the Env.int file.  To get this effect to show up even on +0 weapons on the code before the weapon enchant glow colors change the numbers of EnchantMeshShow and EnchantEffectShow to 0.