A lot of the right advice has already been said, but I'll take a stab at it too because I have some side comments:
Marks (Reds)
: IMO the worst designed runes. The fact is, you basicially just grab the penetration that'll help you more. Most of the reds are just awful. A jungler might grab attack speed, but it's not worth it for a laner since attack speed is a dirt cheap stat.
Seals (Yellows)
: If you have a mana bar, mana regen per level runes are AMAZING. Don't get flat mana regen runes - they cross over at
fourth
level. Garbage. Armor yellows are nearly required for junglers, and are good even just for laners who want some beef. Dodge runes are an acceptable replacement, but ONLY if you have the Nimbleness mastery. Having one without the other is silly, but the two of them combined can be pretty effective. If none of this interests you, CDR yellows are one of the very few out-optimal runes that are still worth taking (in my opinion, at least.)
Glyphs (Blues)
: Fuck I love blues. Blues are the perfect example of what all runes SHOULD be. There are lots of viable blues and it's down to your personal preference. Best of all, as Shanba rightly points out, blues matter little enough for your jungle that even junglers get in on the fun. CDR blues are awesome - I'd avoid scaling CDR, since the crossover isn't until 13. Scaling AP blues are also incredibly useful for AP characters. Don't get flat AP blues - crossover is 5.8, and most AP characters won't be ganking until ult anyway. Magic resist is really powerful, and the crossover level is smart enough (9.9) that both flavors are viable. Flat MR blues will give you a HUGE edge laning against a caster mid. Scaling MR blues are great for a tank worried about slot panic - resistance without clogging a slot is always cool.
Quintessences:
In the old days, HP quints were so dominant that there was no point having other quints. Those days are behind us now, and while health quints are still very powerful, there's room for others. Good replacements include flat AP(the best gold value per rune in the game), AD (but only if you're running 21 in offense), Magic Pen/Armor Pen...lot of room for personal preference. Really, take whatever quint you want. But start with HP because it's a great baseline.
So I'm level 20+ and ready to start this rune thing. What do I do?
You're going to start by picking your 'main' to rune for. Sure, you may play quite a few, but you want a character or set of characters in mind when you rune. Don't make your first a jungler - jungling requires you to be pretty good at reading the gamestate, and it's not a good first thing to rune for.
Then, it goes like this: (remember, when I say "buy a rune", I mean buy a full set of 3/9).
Step One: Buy flat HP quintessences. (Greater Quintessence of Fortitude)
They're no longer the best quints always and forever, but they're GOOD on everyone, which makes them great start quints. You'll be using them on multiple pages. Once you've got a more robust set of other colors, you can get other quints.
Step Two: If you have mana, get Mana regen/level runes. (Greater Seal of Clarity)
There was a GIANT nerf to mana regen yellows (and a buff to base mana to compensate.) Guess what? Mana regen yellows are still
fucking awesome
. If you don't have mana, you can wait on your seals for a while.
Step Three: Get the appropriate red: Either Magic Pen or Armor Pen. (Greater Mark of Insight/Greater Mark of Desolation)
Pretty self-explanatory.
Step Four: Get some nice Glyphs.
Glyphs are awesome, and there are lots of choices. If you use AP and have good ratios, get AP/level (Greater Glyph of Force). If you frequently solo mid/top and don't use AP, get flat Magic Resist (Greater Glyph of Warding). If you're a tank, get scaling Magic Resist (Greater Glyph of Shielding). If none of these things describe you well, go for CDR (Greater Glyph of Focus).
Step Five: If you didn't get Mana regen seals, get another seal.
If you run (or plan to run at 30) the nimbleness mastery, the Dodge seals (Greater Seal of Evasion) are best. Otherwise, pick either Armor (Greater Seal of Resilience) or CDR (Greater Seal of Focus.) Note that Focus seals are STRICTLY WORSE than Focus Glyphs - that's why you don't generally take out-optimal runes. But yellow CDR is still decent if Armor/Dodge/Mana Regen are all somehow not doing it for you.
Congrats! There's your first runepage. Now time to get a second one to expand your horizons...
Step Six: Get the red you didn't get in step 3.
Step Seven: Get Mana regen/level seals if you haven't already.
Step Eight: Get scaling AP blues if you haven't already.
And you should have two pages that look like this:
Page One: Armor Pen / mana if you need it, other seal if you don't / Choice Glpyhs / Flat HP quints
Page Two: Magic Pen / mana if you need it, other seal if you don't / scaling AP glyphs / Flat HP quints
From there, you're on your own, but this is a very good start for runes.
"Don’t buy a dozen eggs if you just want a hardboiled egg. Don’t buy a head of lettuce if you just want a salad. Don’t buy eggs and lettuce if you want egg salad because those are not the right ingredients." -Julius Bloop