Well if I assume that the disease can be spread by means of blood or saliva, then I'd want someone by my side who was able to kill any zombie without a me-lee weapon or waiting for a close combat encounter.
Mordecai, Brick, Roland and Lilith from Borderlands. They would be perfect, it helps to give you cover from all sides and Roland has the Scorpio Turret which would be incredibly useful as it would give us more ammo and help to kill even more of the zombies off. Chell from Portal would also be incredibly useful as she would offer a quick and easy escape route with her Portal Gun offering us the ability through huge distances and to high, safer places in a matter of seconds.
Sylvanas & Tirion Fordring from Warcraft - Sylvanas is undead her selfless and can command them on some level and Tirion is a Paladin who does nothing but smite undead.
Gordon Freeman from Half Life - He's both tough enough to handle zombies and smart enough to be super useful for everything else.
Midna - Just because she's awesome and I'd love to have her around.
Viola/Amy (SC4/SC5), Nightmare (SC5), Link (Adult OoT or TP), Mario, Kirby, Leon S. Kennedy (RE4), Chris Redfield (RE5Gold Warrior), Jill Valentine (RE5 BSAA), Isaac Clarke (Dead Space 2), Rebecca + Hector + Nino + Fiora (Fire Emblem Rekka no Ken), Eirika + Neimi + Ephraim + Colm + Duessel + Knoll + Syrene (Fire Emblem Sacred Stones) would be my team, not including myself of course.
Why would I choose such a huge cast? Fanservice on my part, but a) I expect the apocalypse to be at the very least of Raccoon City level of infection and b) all of them are capable fighters assuming they're in their prime. Viola in VS or VO can pull off amazing combos with the orb. That translates in a zombie apocalypse as zombies being knocked back at least, utterly destroyed at most. She has cons as her orb glows a lot, but all the other cast more than make up for her "hey I'm right here" beacon.