I understand that Zend_Db provides a DBAL, but I'm wondering if it's actually workable to support Mysql and Oracle in the same application.

Mainly, I'm concerned about the difference between Mysql's auto_increment columns and Oracle's sequences for creating surrogate keys. Can Zend_DB help me with this? Or do I need to place a check in my code every time I do an insert to handle Mysql and Oracle differently?

I would suspect you have to check it manually your self. As far as I know, the DBAL doesn't interact with any other, it's free-standing. It just gives you one interface to interact with whatever RDBMS you wish (so switching from mySQL to PostgreSQL to Oracle to MSSQL won't be a hassle).