This post could be better served in the Using Filemaker section. If you want, I can move it there where you can get more attention to your question.
To take a stab at answering it, instead of opening separate DB's, you can use Access privileges to restrict which records a given user can view and/or edit. With those options set, if a user encounters a record to which they don't have accesss, they see it greyed out with "no access" displayed where you would expect to see data. You can then create scripts that help hide the "no access" records from view.
If you click the advanced search link above and search for "record locking" you'll find a large number of posts on this subject with a number of examples.
I'm sorry, I thought since this was a FileMaker Server question for our websites and not an in house thing, this would be the place for it but feel free to move it where you think it would be best answered. Thanks
Reply to your answer...
We briefly considered that but we some of our customers compete with each other and even having those files visible could hurt their buisness as well as ours. So our only option is manually creating a page of links for each cutomer or using the database(s) but only displaying content spacific to the customer while at the same time protecting it so another company can't simply change the address from /companyA to /companyB and gain access to their content. If there's a way of just hiding the files that would be grayed (non-exsesable) to the user that'd be fine.
If you set up record locking correctly, your users should not be able to see any part of a competitor's information. The most they would see is a grey screen with "no access".
Scripts can be set up that hide such "screened" records.
Let's say you have all records with a privilege set name stored in a text field so that all users with a matching privilege set name can view the records but users with a different name are not permitted to view the records.
A script that includes this code (there are a lot of variations possible here):
Enter find mode
Set Field [table:: PrivNameField; Get ( PrivilegeSetName ) ]
Perform find 
Will find only those records not "screened" from view by your access privilege settings.
You can set a script like this to run when a file is opened. If you have Filemaker Advanced, you can use this script to replace the standard "Show All Records" command in the records menu.
That's just a simple example to get you started. More sophisticated scripts can do much more if you need them to.
ah, I understand. Let me run this past bossman.
He assures me that everything is much more complicated than I think because. The page that loads for each building in a customers inventory is populated from 5 different databases... 1 for pricing, 1 for shipping info, 1 for 3D renderings, etc...
The method still works. You just have to set it up 5 times--once for each file.