With 2k05/2k08 it's definitely better to partition a single database. You have all the benefits of storing data like it is in multiple databases while being able to use the functions of a single database, like foreign keys.
That being said, you shouldn't keep everything in a single database. Logically when groups tables don't fit together, I normally separate them into their own databases. For example, I wouldn't necessarily combine place an orders system database and the employee management database together. I suppose there could be reasons to do so, but I am sure you get my point of logically separating data stores where appropriate.
What you should look at is how much the two databases interact. If there are lots of fields which would join across databases, then I would say that it is probably a good idea. If it's maybe one or two fields linking to the employee table, then it might not be worth doing. Your other option is, if the number of joins are small, is to duplicate the necessary tables into the inventory database, especially if it is one table and the two existing databases are large and rather complex.