1st Michigan Inf---27th Virgina captured their flag. (page 495, OR Series 1 Vol 2)
69th new york----Col Radford's (6 companies Virginia Cav)(page 497, OR Series 1 Vol 2)
2nd Maine lost their flag but somehow got it back.

"Colonel Terry, with his unerring rife, severed the halliard, and thus lowered the Federal flag found still floating from the cupoa of the court-house there." (Page 502, OR Series 1 Vol 2)

"He also secured a large Federal garrison flag, designed, it is said, to be unfurled over our intrenchments at Manassas."
(Page 502, OR Series 1 Vol 2)

Johnston's report on page 477, OR Series 1 Vol 2 says: "28 Artillery pieces captured, 5 thousand muskets, a garrison flag and 10 colors were captured on the field or in pursuit."

Beauregard said:
"Some nine regimental and garrison flags were captured"
Page 503, OR Series 1 Vol 2)

The 27th Virginia also captured a "Artillery Battery flag" this must be Griffin's battery flag, since the 27th Virginia captured the battery.

The 8th new york picked up two Union flags off the field.
(Page 428)

The 5th Maine was the extreme right flank regiment of Howard's brigade and the entire Union army.

If I had to guess on the other regiment flags captured, I would say:

1st Minnesota (180 loss)
11th new york (188 loss)
4th Maine (293 loss)
5th Maine (288 loss)
1st Michigan (113 loss) (lost a flag)

All of those regiments were in the 3rd Division. The 3rd Division lost 1,581 men. By far the majority of the total Union loss.

1st Division:
69th new york (192 loss) (lost a flag)
79th new york (198 loss)

*Statement of Artillery lost:
1st US.Artillery Co.G--One-30 pounder Parrot captured.
1st US.Artillery Co.I--All captured (Six-10 pounder Parrot)
2nd US.Artillery Co.D--All captured (2 rifled and 2 smooth bore.
2nd US.Artillery Co.E--Two 13 pounder James and two 12 pounder howitzers.
5th US.Artillery Co.D--One 10 Pounder, two six pounders (old) and two 12-Pounder howitzers.
Rhode Island Battery--Five 13-Pounders.

Total loss: 17 Rifled, 8 Smooth bore= 25 Artillery captured.

If anyone knows of more Union flags captured at this battle, let me know.

Shawn