Unless you really know what you're doing, stay out of the "System" folder and the "Library" folders. The items inside are used by the system and are not intended to be altered by YOU! You actually do alter the items in the Library folders but not directly. By changing preferences in applications and using applications to suit your personal needs, these items are modified constantly. Messing around with these items directly can easily mess things up that are difficult to undo.
When naming files, use only alpha-numeric characters and even avoid spaces if you can. The biggest culprit is the "/". Many people like to name their files by date. This is a bit redundant because the date of the file is already saved within metadata but to many operating systems (and sometimes applications), the "slash" signifies a new directory! This can seriously confuse the operating system. It's like naming your dog "Stay" and calling him to come to you- "Come here, Stay! Come here, Stay!" You'll notice that using the ":" is simply forbidden. Other characters that you should shy away from is the "$", "*", "!". So for simplicity's sake, just stick to the normal alpha-numeric characters.
Fonts have always been a nightmare situation. The thing about fonts is that they get installed at a very low level of the OS so that they are available to all parts of the OS. Often, users become self-proclaimed Graphic Artists by selecting a particular font. Once their brilliance is selected from a library of thousands of fonts, the fonts are never "turned off" again. This can slow your system to a crawl. And if just one of those fonts become corrupt, or its font ID is in conflict with another font, your system can become extremely unstable! Do NOT leave thousands of fonts open at a time. It is well advised that you use a font management program like Linotype Font Explorer X, or MasterJuggler or Font Fusion to manage your massive library of artistic genious- err... I mean fonts. Be sure to look for my article on Fonts for a more comprehensive understanding of fonts.
Email can easily grow to become a problem. Most everyone NEVER ever wants to delete an email. But realize that every email client is nothing more than a database that keeps track of all these emails. Most email clients have a feature to "archive" email messages. Generally, I try to keep my email down to about 1,000 email messages. Once it grows beyond that, I archive everything but the last 3 months. I don't think I've ever needed an email beyond that and if I did, I could always go back to the archive.
Save ALL files within your home directory! Do NOT save items to the hard drive directly. This will not result in any performance hit but when backing up your system, when all files are within your home directory, it is much simpler to back up and permissions are as you would expect them to be. There really is no reason to save things outside of your home directory. With this said, Leopard has the BEST backup software built into the OS called Time Machine. Use it!! All you need is an external hard drive.
Keep your OS up to date. You don't need to download and install the updates the first day they come out but trust Apple when they say it resolves issues. It is true that occasionally things break after a so-called update is released. But more often than not, it fixes certain things under the hood that you don't even realize. And, if you've got a Time Machine backup going, you risk very little because you can always "roll back" to a previous state.
Applications are also updated frequently. Make sure that they are up to date as well.
Most importantly- be flexible. The term "computer science" implies that this is a science and perhaps in an ideal world where we were all scientists, this would apply. But I like to think of my Mac as a living organism. There are growing pains, sickness and heartache. Understand that and do not let the little things compromise your workflow. The computer should increase your performance and not hinder it. If that means you must buy a second computer to ensure full productivity, so be it. Otherwise, always have a plan B.
There are 3 things that you should do on a regular basis to keep your Mac in shape. And, it only requires 2 applications.
Disk Utility comes with every Mac and can be found in the Applications/Utilities folder. With this application, you can verify your hard disk and repair disk permissions. I would do this about once per month. Run Disk Utility and select your startup disk which should be the very first item in the left column.
Once your hard drive is selected as shown in this picture, go to the bottom right of the same window and hit the "Verify Disk" button. This will take about 2 or 3 minutes and will verify that all of your "volume directory" information is in order. The Volume Directory is like a table of contents of a book. It tells the hard drive where all of your files are. If this becomes corrupt (which will happen over time), your computer can become unstable, slow down and crash frequently. If left unchecked, your hard drive can become unusable and you risk all of the data on your drive. This is why it is so important to check this about once per month. If you find that something is indeed wrong, you must take immediate action! Simply restart your computer while holding down the "Shift" key. This will force the computer to fix the volume directory prior to loading the OS. So the computer may take up to 5 minutes to start. This is normal. This is known as starting up in "Safe Mode" and will disable all 3rd party extensions and unnecessary fonts. Simply restart your computer again to get out of Safe Mode. If you verify the drive again, you should notice that all problems have been resolved. If not, contact me!
While you're in Disk Utility, you might as well also "Repair Disk Permissions" which is a button that is available on the same window. I don't normally "verify" first, I go straight to repair. This is most needed after performing an installation of some program or driver. Printer drivers and QuarkXPress are huge culprits! Incorrect permissions can cause a system to slow down or applications to crash. This can take up to 20 minutes but most often can complete in about 5-7 minutes.
And lastly, the only 3rd party application that I like to recommend is something called YASU. It stands for Yet Another System Utility and as the name implies, there are a handful of applications that perform the same tasks as this. I just happen to like this one a lot. It is shareware so please send the programmer the suggested $3.50. In fact, throw him a full 5 spot because his app is really that good. And, he's got a great website too.
Again, depending on how much you use your computer and how (I run this once per month), check all items and then hit run. The most important thing this program does is it clears cache files and font caches. Often, this resolves font related issues and system instability.
And something to watch out for: Do not let your startup disk get fulll! Don't even let it get close to getting full. As a general rule, you want to keep at minimum, 10% free. But the more multimedia stuff you do, the more free space you'll need. Like if you're making movies or music, you want your drive about 50% free. So if your drive is filling up to the point where less than 10% is free, you will definitely notice your system starting to slow down.
And that's it! That is all I do on a regular basis!