1. The Tortillas - Chipotle's are thicker and chewier; Qdoba's are thinner and stay out of the way of the fillings.
2. The Sauces - Chipotle has the basic fillings (e.g. chicken, beef, pork, etc.) that come only plain; in addition to plain Qdoba offers those with tasty sauces including Ancho BBQ and Poblano Pesto, among others.
3. The Rice - Chipotle has way too much cilantro in its rice; Qdoba has a more reasonable amount. For me and people like me (www.ihatecilatro.com) better to have less (or none) and let those who love cilantro add more.