Why such a problem? Well, in short, fonts are tiny little pieces of code but their power (for good and evil) lies in the fact that that tiny little piece of code is used in every application as well as your system. Fonts are overlooked as little, innocuous extra bits that sit there and don't do much until called upon. Partially true, but for the most part...not. Every font that is active on your system is sitting there right at the top of every program waiting. Waiting, but active.
There are typically 4 issues that I encounter. First, font corruption. Pretty simple. The font is just messed up. It has been corrupted by being copied here and there, emailed, or simply was never 'good' in the first place. Designers are quick to hop online to a free font site and start downloading fonts, but all it takes is one small piece of bad coding to throw your entire system for a loop.
The second problem is font conflict. Meaning that a particular font is somehow interfering with the code of another font or an application. This is particularly troublesome to troubleshoot because it requires figuring out which font is doing the interfering. Not always as easy as it sounds. Easier when employing proper font management (more later).
Third, duplicate fonts. In a way, this is also a bit like a font conflict. You've got 2 fonts running that have the same name or ID. Your system thinks, "Huh?" and tries to pick and choose, usually resulting in some pretty bad stuff.
Lastly, and all too common, too many fonts active. The limit on active fonts on systems prior to OS X was 128 (for obvious addressing reasons). That limit is no longer an issue in OS X. However, limiting the number of fonts that are active greatly reduces the chances of conflicts occurring. It's science!
So, where does one begin in getting control of fonts? Personally, as soon as I sit down at someone's machine to solve a system/application problem, I immediately ask about how they are managing their fonts. which is usually responded to with a blank expression. And that tells me that I'll likely find one of the above issues.
The average Joe Mac user should get along fine with the OS's application Font Book. It's simple and easy to use. And assuming that the user doesn't have a ridiculous amount of fonts, leaving them all on at all times is certainly an option. Although I never recommend it. For the designer, however, something more, well, professional is required. I don't really care which font management software you use. They're all pretty decent. Font Agent, Suitcase, and FontExplorer just to name a few. I prefer Font Agent. It's lean, cheap, and does the job quite nicely without a million different settings to get in the way.
Once I've thrown Font Book in the trash, emptied the trash, and then restarted, I look to a few places to see what's going on. First, I check out /Library/Fonts. This folder should be empty...it won't be. I remove all fonts from this folder and place them elsewhere on my hard drive. Then I check /Users/Administrator/Library/Fonts. This folder should also be empty...and also will not be. Many installers place their own fonts in this folder (particulary MicroSoft products) so you should check it fairly often and after any install. Place these fonts elsewhere. Now, the sensitive part. Look in /System/Library/Fonts. These are the base fonts that your system uses. NEVER (unless you really know what you're doing) remove fonts from this folder. Early on in OS X, I made that mistake...cleaning it out as I do all other folders. The finder will not launch. Correcting the stupidity takes some pretty fancy footwork in single user mode. Not for the faint of heart. IF there is a font that is really causing you a conflict with your own fonts, then you can consider removing that one font. This is particularly difficult in Leopard, as the system automatically replaces the font...to stop the unwary from making my mistake. This can be gotten around, more on that here.
Now you can restart your computer and should be operating with the bare minimum fonts and likely whatever crash problems, etc. that you had will have disappeared. The secret to good font management is simply keeping the least amount of fonts in your system folder as necessary and keep all your fonts elsewhere on your machine and activate them with a font management app as needed. Using your font management software you can now turn fonts on and off and track down problems. Most popular font management apps will check for issues once you import the fonts into them.