When you say custom table - you don't mean custom table in Kentico sense ?
With Kentico custom tables it is not possible because a custom table must be located in Kentico DB. You can do it with modules: module custom table can point in an external DB, you just need to specify an external connection string in web.config. When you define module classes and you need to use connection string for external DB in your module class :).
Another way is to use SQL Data Source Web part and point to a SQL server your want. This is an easier way and you don't have module complexity.