Tier 1 runes are fine buys if you know what to get before hand, especially being as cheap as they are.
Tier 3 are expensive, but worth the price because of the stats you get.
Tier 2 are sort of IP sinks. If you plan on filling a page pre 20 use Tier 1's. Otherwise, continue savinng up for when you hit 20.
Armor pen and Magic Pen Reds are always safe buys as they can be used on pretty much every champion. The same goes for Armor Yellows.
I recommend looking at the per level runes as well. Some become stronger than the flat runes only after 9 LEVELS! This will put you more towards mid game resistances. However many of them (AP per level blues for example) become stronger by level 7.
Flat AD is better early as it will vastly improve poke and last hitting.
Scaling AP is better because it allows you to scale with each level (AP carries gain more and more damage with every rank of a spell, so the scaling runes will improve this further).
Quints, as a general rule of thumb should be Flat. They have the highest values, so they are best used to pad early game stats, or something that will be effective well into late game (Flat HP, Movespeed, Gold per 5, AD, AP, etc).
EDIT: what I've said is by no means Gospel, just try to consider what will be needed. Will you pad your early game, in hopes of getting ahead early. Or try to play towards a slightly stronger late game.
Basic build for an AD
Armor Pen Reds
Flat Armor Yellows
Flat/scaling MR Blues
Flat HP/AD Quints
Basic build for an AP mid
Magic Pen Reds
Scaling Mana Regen Yellows
Scaling AP Blues
Flat AP Quints