First question would be, what are you using for a font manager? For the type of work you do, Font Book should be just about your last choice. Suitcase Fusion 3 or FontExplorer X Pro are the ones I recommend.
If you already are using Suitcase or FEX Pro, then get Font Book off your Mac. Having more than one font manager on any system is a sure way to make controlling fonts difficult.
1) Open Font Book, and then its preferences. Uncheck the box for "Alert me if system fonts change". Close the preferences and shut down Font Book. Put the Font Book application in the trash and delete it.
2) Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding it until OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally.
This will reset Font Book's database and clear the cache files in your user account. Any font sets you have created will be gone. Also, all fonts in the three main Fonts folders (System, Library, your user account) will now be active, regardless of their state beforehand.
The main goal in this step is to remove the orphaned Font Book database from the hard drive. With the Font Book application no longer on the hard drive, a new one cannot be created. Which is what we want.
3) Close
all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:
sudo atsutil databases -remove
This removes all font cache files. Both for the system and all user font cache files. After running the command, close Terminal and
immediately restart your Mac.
because a lot of the displays on certain browsers and programs are not displaying like they used to.
That comes back to font cache data that no longer relates to a font still on the drive. Clearing all font cache data after manually removing any fonts is pretty much a must. As is resetting Font Book's database by doing a Safe Mode boot.
Ever since I did that, InDesign CS4 is NOT seeing any T1 fonts. Before, it was only a Helvetica Neue T1 issue.
I'd say something on the system is goofed up. When I first installed Snow Leopard to an erased partition, all fonts worked. I did my usual of removing Font Book and getting the fonts on the drive down to the minimum. I then started installing all of my third party apps. Somewhere in there, fonts simply stopped working. The only fix was to reinstall OS X and reapply the Combo updater, along with whatever else Software Update said was needed. Voila, fonts worked again as expected. Just had to remove Font Book and all the fonts I didn't want on the drive again.
It's a bit of a pain to do, but that's why I went right to "reinstall the OS" above.