Michael Matthews, Diego Ulissi, and Giacomo Nizzolo have raced against both Oscar Freire and Marcos Freire. There are probably others in the current peloton who have done so too, but those were the first ones I could identify.
Arnaud Démare raced against Óscar at races like Gent-Wevelgem, GP Fourmies and Paris-Bruxelles in 2012, Freire Sr's last season.
Davide Cimolai will have faced Óscar at E3, Gent-Wevelgem and Ronde van Vlaanderen that year too, and
Marco Haller faced him at Dwars door Vlaanderen, the World Ports Classic, GP Fourmies and Paris-Bruxelles.
Vegard Stake Længen faced him a lot that year, racing Milan-San Remo, Flèche Wallonne, LBL, the World Ports Classic, Paris-Bruxelles and Fourmies, while
Adrien Petit might have faced him most, doing Dwars, E3, Gent-Wevelgem, World Ports Classic, Paris-Bruxelles, Fourmies and Wallonie.
Nairo Quintana will have faced Óscar, but only at the World Championships Road Race in 2012.
Florian Sénéchal also raced the World Ports Classic in 2012, while
Gianluca Brambilla will have faced him in Tirreno-Adriatico in 2011 and 2012.
Mikel Bizkarra did the Challenge Mallorca races in 2011, and in three of them (Palma, Cala Millor and Palmanova) he faced Óscar Freire.
All of those also did Challenge Mallorca races this year against Marcos Freire.
Larry Warbasse didn't, but he did race the Gran Premi València one-day race before it, and faced Óscar Freire at the 2012 GP de Wallonie;
Baptiste Planckaert also did that race against Marcos, and faced Óscar at Dwars, E3, Ronde, World Ports Classic and Fourmies during his Landbouwkrediet days.
Alessandro de Marchi likewise raced Marcos in Valencia and Óscar at Milan-San Remo in 2011.
I think I've caught everybody thus far, obviously some more are going to join the ranks in the coming months most likely.