Despite having won the Derby, Winning Colors was overshadowed later in the year by the unbeaten filly Personal Ensign.
Several that I consider "All Time Greats" are:
Gallorette (who mostly raced males)
Two Lea (very underrated filly)
Go For Wand
My Juliet (exceptional sprinter)
Bold 'n Determined (who was the same year as Genuine Risk, and may have been better)
A note on criteria: I am focused mainly on US based fillies and mostly on dirt runners as it's (somewhat) easier to compare horses of diferent era when you can at least compare the quality of races they ran. I also leaned toward mares with a long record of consistency rather that those that blossomed and we exceptional "for a time."
Resident racing historian ~~~ Re-riders Clique
Founder of the Mighty Thoroughbred Clique
Possibly the greatest of them all was Sceptre.
She ran in all five English classics, winning four of them. Beat the boys in the 2000 Guineas, then won the 1000 Guineas a couple of days later against the girls. Ran in the Derby, finished 4th. Then came out two days later and won the Oaks over the same course and distance, 12f at Epsom (and people say you can run a horse twice in a week!). She then capped the year off by beating the boys in the final English classic, the St Leger.
That's a racehorse.
Mumtaz Mahal, Moccasin, Landaluce, Terlingua, Safely Kept. Kincsem is outside the 100 time frame, but it's a shame she is not better remembered: undefeated in 54 starts. Why is she not spoken of with the same reverence as Man O'War, Eclipse or, at least, Colin?