There is a certain elegance in a well-designed rule: balanced, easy to understand, consistent, and concise, a good rule makes playing a pleasure. The writers of the D&D core books really rolled a natural 20 on that craft check.
Side note -- I'm always leery of non-core supplements, myself. I always find something broken or, at least, inelegant in them. YMMV, of course.
And when you put your hand to creating rules of your own, strive to hit the same level of quality and elegance. That may not seem easy, but there are resources out there to help you. I mentioned Monte Cook's design workshops in an earlier screed, and they are excellent. Here are a couple more places for ideas.
For more on prestige class (PrC) design, check out this Wizards of the Coast message board thread on "PrC Construction and Balance (and finding one for your character)." I added to this discussion myself, so you can see my thoughts on this in the thread.
For a good guide to writing new spells correctly, check out an article by Mike Mearls on "So You Wanna Design a Spell." Mike's purpose here isn't to offer advice on balanced spells, but to get the form right.
That's key. Game balance is only a part of a well-designed rule. Correctly following the proper structure, syntax, and style makes a rule elegant. It's like writing a sonnet: following the correct rhythm and rhyme scheme won;t make it a great sonnet, but if you don't, it will be a bad sonnet, no matter how beautiful the theme and words.
Take feats, for example -- if your feat has a required ability score, it has to be an odd number. Or prestige classes -- if your PrC requires a certain skill, make sure that the required skill is also a class skill. Or sonnets -- if it's not 14 lines of iambic pentameter, it's not a sonnet.
The easiest way to make sure that your new creation follows the rhythm that makes core rules elegant is this: Make A New Rule Like An Existing Rule. Start with an existing spell, feat, race, prestige class, whatever. Then start swapping things in and out. If you add an ability, take out an ability of about the same power. After a few substitutions, you'll be well on your way.
And when you are done, it always helps to get some feedback. Try posting your ideas online for others to comment on. Here are a few Internet communities that have active discussions and people who will tell you what they think: