Basic AP:
Marks: x9 Magic Pen
Seals: x9 Armor (x9 scaling health is also good on risk takers like kat)
Glyphs: x9 Flat mr (x9 AP is good when vs AD Lane)
Quints: x3 AP
For ad Junglers like Lee, You want to go:
Marks: x9 AD
Seals: x9 Armor
Glyphs: x9 Flat or scaling MR. Depends on if you have an early or late game champ
Quints: x3 AD (x3 Attack speed is good on champs with a passive that activates on hit, such as Yi and Warwick.)
Top lane runes are basically the same as the jungle ones, depending on who you play. For people like singed, many like to bring along Mana regen blues. But you don't really need to get into that unless you get any more rune pages, which I highly recommend you do, whether you get them with IP or RP. If you are going to spend money on runes, it might be worth it to go the extra way and purchase the 7 Rune Page bundle. Using anymore RP on rune pages after that is unnecessary IMO.
If you have any other questions or want any tips on certain champions and their runes you can add me in game. IGN: fishingl3g3nd
Goodluck in the fields of justice,
-- Fishing