Yeah, windows has major issues with consistency in fonts. The number one problem is exactly what you're saying, just dropping fonts into the font folder without the "install" function. Points to one of my major underlying dislikes of Microsoft development ethic... "If it's not broke, don't fix it. If it is broke, don't fix it. If it breaks something else, blame open source developers".
Two things to think about in regards to fonts.
1. Do you really need them? Without a good background in typography and design, over using fonts or using the wrong fonts can be a problem. If you just "like fonts" like I hear from a lot of people (myself included when I first started working with graphics) you might just collect them as you find them. This is fine if you use them sparingly (and don't mind the fact that it's adding scads of time to your boot time, application launch time, and menu load time). I saw some figure recently saying that a professional designer will have 1-200 fonts on their system, while a professional typographer will have 1000-1200. Considering there are something like 300,000 accepted font styles, this would lead me to think that MOST fonts aren't necesarry. Most common fonts come WITH the computer to begin with. You have 40-50 fonts installed on your system when you install the OS. Some of them are pretty good and have been around for years and years. There is a reason why certain fonts are installed with every copy of windows, mac os, and even when you install Photoshop. Outside of that is generally special projects... which brings me to thought number two...
2. Get a font manager. Xd already mention this briefly, but if you decide that you need that many fonts then consider purchasing a font manager. I've never used "font thing" before, but I've heard it's decent (is it free? that'd be ever better). On Macintosh, the most widly accepted manager is Extensis Suitcase. It's completely Jaguar ready now (for those of you keeping score). For those of you that haven't worked with something like suitcase before; a good font manager will allow you to have MINIMAL fonts installed directly into your system so your load times are low and memory overhead is low on application launch. But you can set up scenarios for fonts to be loaded. First off... you can load and unload fonts INSTANTLY... so no rebooting to see fonts. You can place your fonts into sets for better organization (when you start having THOUSANDS of fonts, this can be a big deal). You can set certain SETS of fonts to load at boot time, certain sets to launch automatically when you start up specific programs (say... Photoshop... or Illustrator?) If you had a font from a client that you ONLY needed for that client.. you could have it in your list and only launch it when you needed that specific font. I've worked mostly with Suitcase, so I can't speak for the features of other software, but it will tell you when you have a font that isn't in a document AND LET YOU LOAD IT RIGHT THERE. Anyone that's worked with documents from another independant designer before knows the headache it can be when you get a document full of fonts you don't have. Suitcase also will tell you when you have duplicates or font conflicts as you load a program and lets you resolve them during launch rather than having to shut down, fix the problem, and restart... only to find another problem. One other "nicety" is that you can set Suitcase's preferences to show PREVIEWS of fonts in their font names in EVERY application on your system. So when you launch Illustrator... and you open that massive font list... and you can't remember the differences between Mistral and Minstral... you get the font face preview as PART of the name. Very convenient at times, especially when working on someone else's computer where you are unfamiliar with the fonts.
I know, it's starting to sound like a sales pitch... really, it doesn't matter which software you pick as long as it does what you need. Personally, I've found that I just don't need that many fonts, so rather than having the overhead of lots of fonts or a manager, I've strayed away from using custom fonts for every project and focussed more on layout, design, and appropriate font choices. The short version of this is... if you NEED lots of fonts, it's worth 50-90 bucks to get a professional font manager.
It's only after we've lost everything...
That we're free to do anything...