Goldikova is the only 3-time Breeders' Cup winner, and finished third when trying for a fourth win in the Mile in 2011.
The list of horses who have won two Breeders' Cup races over the first 34 runnings isn't very long, although with the event expanded to 13 races now it may grow more quickly now than in the past. Here are those elite horses who have managed to win twice or more:
Beholder - three victories, one in the Juvenile Fillies and two in the Distaff
Goldikova - three victories in the Mile and a 3rd place finish when trying for four
Bayakoa - two victories in the Distaff
Conduit - two victories in the Turf
Da Hoss - two victories in the Mile plus a 13th place finish in the Sprint
Goldencents - two victories in the Dirt Mile
High Chapparral - two victories in the Turf, although the second was a dead heat
Lure - two victories in the Mile as well as a 9th place finish in his last try there
Midnight Lute - two victories in the Sprint
Miesque - two victories in the Mile
Mizdirection - two victories in the Turf Sprint
Ouija Board - two victories and a 2nd in the Filly & Mare Turf
Royal Delta - two victories in the Distaff
Secret Circle - a win the the Juvenile Sprint and the Sprint
Stephanie's Kitten - a win in the Juvenile Fillies Turf and the Filly and Mare Turf
Tiznow - two victories in the Classic
Wise Dan - two victories in the Mile
Zenyatta - a win in the Ladies Classic and the CLassic and she will try the Classic again in 2010
There are quite a few more with one win and one or more near misses. Here is a list of the horses with a win and a 4th place or better finish to go with it. I didn't note the years these occurred in, but if you are interested, you can get the full list of multiple year Breeders' Cup starters here.
Kona Gold started in the Breeders' Cup Sprint five times, finishing 1st in 2000, 2nd in 1999, and 3rd in 1998.
Street Sense won the Breeders' Cup Juvenile in 2006 and became the first winner of that race to also win the Kentucky Derby. He went on to finished 4th in the 2007 Breeders' Cup Classic.
Alysheba - 3rd Juvenile, 1st and 2nd Classic
Ashado - 2nd Juvenile Fillies, 1st and 3rd Distaff
Banks Hill - 1st and 2nd Filly & Mare Turf
Better Talk Now - 1st, 7th, 2nd, and 4th Turf
Black Tie Affair - 8th and 3rd Sprint, 1st Classic
Buck's Boy - 4th, 1st, and 3rd Turf
Cardmania - 12th, 1st, and 3rd Sprint
Cat Thief - 3rd Juvenile, 1st and 7th Classic
Chief Bearhart - 11th, 1st, and 4th Turf
Chief's Crown - 1st Juvenile, 4th Classic
Cigar - 1st and 3rd Classic
Cozzene - 1st and 3rd Mile
Curlin - 1st and 4th Classic
Dance Smartly - 3rd Juvenile Fillies, 1st Distaff
English Channel - 5th, 3rd, and 1st Turf
Escena - 3rd and 1st Distaff
Fly So Free - 1st Juvenile, 4th Classic, 9th Sprint
Forever Together - 1st, 3rd, 6th Filly and Mare Turf
Fraise - 1st, 4th, and 11th Turf
Gilded Time - 1st Juvenile, 3rd Sprint
Indian Blessing - 1st Juvenile Fillies, 2nd Filly & Mare Sprint
Storm Flag Flying - 1st Juvenile Fillies, 2nd Distaff
Street Sense - 1st Juvenile, 4th Classic
Theatrical - 1st, 2nd, and 11th Turf
Thirty Slews - 1st and 4th Sprint
Unbridled - 1st and 3rd Classic
Ventura - 1st and 2nd Filly and Mare Sprint
Very Subtle - 1st and 4th Sprint
The list of Breeders' Cup winners who have gone on to have winning offspring includes only 19 stallions and 3 mares. There are two families that seem to have good luck with Breeders' Cup winners. Classic winner Unbridled has sired three winners, and his son Unbridled's Song, who won the Juvenile, has sired five winners. Distaff winner Personal Ensign's daughter My Flag, who won the Juvenile Fillies, also has a daughter who won the same race. Below is a list of the winners and their winning offspring. You can view the full list of sires of Breeders' Cup winners here.
AP Indy (Classic) - Tempera (Juvenile Fillies), Eldaafer (Marathon)
Review: Crushing the Cup 2016 - by Jim Mazur and Peter Mallett. An invaluable tool for trying to unlock the mysteries of handicapping the Breeders' Cup races. Updated for 2016, this is their 25th anniversary edition and they will have a new edition for 2017.
The Breeders' Cup Championship Day - The official page for the Breeders' Cup championship races. Just about anything you need to know about it: results, video clips, and race calls for past years, and eventually nominations, entries, and results.
Free Prep Replays - for major prep races in the Breeders' Cup Challenge. The ones with camera logos have video available.
Breeders' Cup Supplemental Entries - The old official policy on supplemental entries plus all the supplemental entries and how they fared, mostly it was a losing proposition. There are no more supplements now, only late nominations making it impossible to track since the change.