HoMM2, without a doubt.
The first one is a classic that deserve to be revisited by any fan of the series but graphically it's unpolished, and factions are very unbalanced.
The third one has tons of heroes, each with their own class, skills, bonus and penalty, there are hundreds of artifacts, spells, units, many which all look alike, just like the castles, just like the land tiles... Don't get me wrong, HoMM3 is clearly the main dish when it comes to the HoMM series, but it's not the entry.
IMO, the best game to get into the series and learn the basics is the second game. It's more polished and more balanced than the first game. Nearly every game elements from the third game are present in the second game, but in much smaller quantity, making things easier to learn and memorize, and with the colorful 2D graphics of the second game, units, heroes, castles and land tiles are also much easier to recognize.
Start with HoMM2 to learn how the series works, learn the basics and develop some tactics that will help you in the other games. Play a bunch of scenarios, give the main campaigns a try (but stay away from the Price Of Loyalty campaigns, they are shorter but they are also much harder) and when you feel you know enough about the game, make the jump to the HoMM3.
Story wise, there is nothing to worry about. Like DarrkPhoenix said before, the plot is not the main reason why people play these games. Decades span in between each games and their addons, each campaigns tell different stories, with different characters and locations, there's no need to play the previous games or the M&M games to have fun with HoMM games.
Post edited July 26, 2010 by blueskirt