Why are my fonts not showing up in applications?

Back up all data.

Launch the Font Book application and validate all fonts. You must select the fonts in order to validate them. See the built-in help and this support article for instructions. If Font Book finds any issues, resolve them.

From the application's menu bar, select

File ▹ Restore Standard Fonts...

You'll be prompted to confirm, and then to enter your administrator login password.

Boot in safe mode to rebuild the font caches. Boot again as usual and test.

Note: If FileVault is enabled, or if a firmware password is set, or if the boot volume is a Fusion Drive or a software RAID, you can’t boot in safe mode. In that case, ask for instructions.

Also note that if you deactivate or remove any built-in fonts, for instance by using a third-party font manager, the system may become unstable.

Agree with Linc. If those apps see all of the fonts, then they all should.

MS Office does keep its own separate cache files. It shouldn't matter if they're damaged, but ya' never know. Try clearing them out.

Shut down all Office apps (I'm presuming Office 2011 here). Then go to the folder:

~/Library/Application Support/Microsoft/Office/Preferences/Office 2011/

(the leading tilde means your user account) and delete the file:

Office Font Cache

Launch any Office app to rebuild its font cache.

I'll have to think on the PS issue.

What you're seeing is very typical of a trashed Font Book database. Not the only possible cause, but at least 90% of the time.

Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until you see a progress bar towards the bottom of the screen. You can let go of the Shift key at that point.

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 clear Font Book's database and the cache files of the user account you logged into in Safe Mode.

the fonts are all loading fine in TextEdit and Pages

That pretty much rules out a font issue as such. I don't use MS or Adobe products myself, so I don't think I can contribute much more.

Problems such as yours are sometimes caused by files that should belong to you but are locked or have wrong permissions. This procedure will check for such files. It makes no changes and therefore will not, in itself, solve your problem.

First, empty the Trash, if possible.

Triple-click anywhere in the line below on this page to select it, then copy the selected text to the Clipboard by pressing the key combination command-C:

find ~ $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 \) 2>&- | wc -l | pbcopy

Launch the built-in Terminal application in any of the following ways:

☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)

☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.

☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.

Paste into the Terminal window (command-V). The command may take a noticeable amount of time to run. Wait for a new line ending in a dollar sign ($) to appear.

The output of the command will be a number. It's automatically copied to the Clipboard. Please paste it into a reply.

Forgot to add an annoying thing Office does. If at any time you disable or enable new fonts, you have to shut down and relaunch the apps before they will recognize any change to available fonts.

Some of your user files (not system files) have incorrect permissions or are locked. This procedure will unlock all your user files, reset their ownership, and remove their access-control lists. If you've set special values for those attributes, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it.

Back up all data.

Step 1

If you have more than one user account, and the one in question is not an administrator account, then temporarily promote it to administrator status in the Users & Groups preference pane. To do that, unlock the preference pane using the credentials of an administrator, check the box marked

Allow user to administer this computer

Then reboot. You can demote the problem account back to standard status when this step has been completed.

Enter the following command in the Terminal window in the same way as before (triple-click, copy, and paste):

{ sudo chflags -R nouchg,nouappnd ~ $TMPDIR..; sudo chown -R $UID:staff ~ $_; sudo chmod -R u+rwX ~ $_; chmod -R -N ~ $_; } 2>&-

This time you'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.

The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.

Step 2 (optional)

Take this step only if you have trouble with Step 1, if you prefer not to take it, or if it doesn't solve the problem.

Boot into Recovery. When the OS X Utilities screen appears, select

Utilities ▹ Terminal

from the menu bar. A Terminal window will open. In that window, type this:

res

Press the tab key. The partial command you typed will automatically be completed to this:

resetpassword

Press return. A Reset Password window will open. You’re not going to reset a password.

Select your startup volume ("Macintosh HD," unless you gave it a different name) if not already selected.

Select your username from the menu labeled Select the user account if not already selected.

Under Reset Home Directory Permissions and ACLs, click the Reset button.

Select

 ▹ Restart

from the menu bar.