Completely different games. Organ Trail is essentially a tongue-and-cheek spin on The Oregon Trail. Rebuild is a turn-based strategy game in which you need to expand your (non-zombified territory by recruiting other survivors, salvaging, and slowly taking back control of the city. You can play it (and possible Organ Trail) on kongregate dot com.
Organ Trail... No contest. Different games, true, but Organ Trail is a lot better than Rebuild for me.
Exact-Psience My 2014 Top 10 Games of the Year: Monster Hunter Freedom Unite, Hearthstone, VVVVVV, Battleheart Legacy, Wayward Souls, Bug Heroes 2, Powerpuff Girls Defenders of Townsville, Deep Loot, Monument Valley, Bioshock Honorable Mentions: Traps N Gemstones, Bardbarian, Goblin Sword
I prefer Rebuild myself but agree with Greyskull that it's hard to directly compare these two. If the original poster is just looking for a good zombie themed game then both are worth picking up along with Zombies. (pixel dual stick shooter, by bignic), Crazy Bill (auto-run platformer, free), and the Infect Them All (sidescroller/arcade) series are worth looking into.