Ah the dreaded Veto power of a commish.
I'm a commissioner too of a Private Yahoo Roto League and I don't like vetoing trades either but I'll give you my opinion on the two trades you've posted.
Hank Blalock, Torii Hunter, Juff Suppan for Randy Johnson, Eric Chavez, Carlos Lee
Personally I'd love to be the team getting Johnson, Chavez and Lee, and I'm assuming this deal was proposed because Johnson is on the DL. But he's coming back in June, and should be back to full strength. So to compare the players, I'd say Randy is better than Suppan, who pitches for the Pirates, Chavez is better than Blalock since Blalock doesn't hit left handers, and Carlos Lee is even with Hunter since Hunter isn't stealing bases.
Veto the trade.
Erubiel Durazo, Shawn Chacon, Joe Nathan for Albert Pujols, Jose Jimenez, Billy Koch
Simply put, Pujols is worlds better than Durazo AND has 3 position eligibility. Chacon is riding high right now, but history says he'll come back down to earth soon, and I'd rather have Koch than Joe Nathan. What good is a middle reliever in a head to head league?
I'd say Veto