In 2002, when the Angels defeated the Giants in the World Series, both teams were wildcards (and as there was only one wildcard, the bottom seed by default, though they were not the lowest win totals as Minnesota had 5 fewer wins than Anaheim, as Central Division champions). That is the only example in Baseball, though there really have only been two decades of history where it would be meaningful to say the two lowest seeds faced each other; prior to the wildcard, you only had one team from each division (so 4 total teams) in the playoffs, and with divisional play it's hard to say who would be seeded what in a larger playoff.
The NHL and NBA have longer histories of large seeded playoffs. In the NHL, never have two 8 seeds faced each other, but in 2012 the Kings (8) beat the Devils (6) for the first 8 seed win in NHL history and the largest sum of seeds in the Finals history.
In the NBA, 8 seeds nearly never beat 1 seeds; the 1998-1999 New York Knicks remain the only 8 seeds to reach the finals, losing to the Spurs (Duncan and Robinson's first championship). The lowest seed to win a championship was the Rockets in 1994-95 (6 seed), but they beat the top seeded Magic that year. No other team higher than 4th has ever won a NBA Finals.
In the NFL, there have never been a particularly low combination. Although 6 seeds have been successful, for example in 2005 PIT (6 seed) defeated SEA (1 seed), they've never had to face similarly low seeded teams; the lowest I see is 6 seed vs 2 seed (Packers/Steelers), which isn't exactly a low seeded combo either.
