First off, some caveats.
- This is strictly a comparison with how much it would cost to get those stats via in-game items, and I've looked at the cheapest objects. As a fictional example, the Sapphire Crystal gives 200 mana for 400 gold, let's say a rune existed that gave you 20 mana, this would mean that rule would be valued at 40 gold. I make this point as just because something is worth a lot of gold does not mean it is always the best choice.
- I am most looking at flat runes. Comparing with the scaling runes would be more difficult and more open to interpretation. I will however make some references to scaling runes where appropriate.
- There is no simple cheap item that gives only armour pen or only magic pen, so I have excluded those runes from my analysis. One quick point to make on these though - the runes that give you armour & magic pen were not nerfed as much as the ones that only give you one of them, which I think makes them a very good choice if you will do a fair bit of damage in both categories (eg Teemo, Corki).
- I'm only looking at primary runes, obviously.
OK, with those out of the way...
Marks
There are 5 main sorts of marks. Armour pen, magic pen and armour plus magic pen are all being ignored as mentioned above. This leaves us with AD and AS. AD is a decent choice. I saw some analysis of AD vs Armour pen which argued fairly convincingly that 90% of the time, armour pen was better, however since they have been nerfed, I would imagine AD is a more realistic choice now.
However it's Attack Speed that is the standout here. They have become great runes in Season 3 as a result of changes to items, which have made attack speed items more expensive. For example the dagger has dropped from 15% to 12% as (with a very slight drop in price too). If you look at my spreadsheet, you can see AS runes are the best value quints and best value normal runes too. If you took all AS quints and marks, this would give you +25.5 % attack speed, equivalent to an in-game cost of 750 gold. Brilliant or what? In fact, AS is such good value that you can get seals and glyphs of them too, and they are still decent value, Seals are worth 25.33 gold and Glyphs are worth 21.33 gold, which is comparable to, say, flat AP runes.
Seals
No surprises here. Armour is narrowly the best, (28 gold) and is probably the most chosen Seal. Mana regen is also a decent choice at 24.6 gold, and is better than the scaling rune until level 7, by which point you're unlikely to be running out of mana anyway.
Health and health regen are awful, being worth a paltry 14-15 gold, and scaling health becomes better at ranks 4-5. There's nothing these will do for you that a health potion or 2 can't.
Glyphs
Mana regen, magic resist or CDR are the main options here. They are all worth about the same. Magic resist is marginally the best and is picked quite often, though magic resist scaling will beat it after level 9. This shows up the randomness of the numbers on runes - why does the armour scaling runes beat the armour flat rune at level 10, but for magic resist it's level 9? It doesn't make sense!
The other option is flat mana, but having looked at the numbers for Singed, it wasn't really worth it. You're probably better off buying a mana potion or two.
Quints
Firstly, three general things about Quints... firstly there are all decent value for money (mostly between 80 - 120 gold), and secondly scaling quints seem to take longer than normal runes to catch up with flat runes, so the majority of the time I think it is better to get flat quints. Finally there are loads of other quints that do all sorts of different things but I'm sticking with the main ones here. The Gold per 10 and the movement one are ones I do use on some of my pages.
OK, so the best quint, as mentioned earlier, is the Attack Speed one. Close behind in second place, and the only other one worth over 100 gold, is the flat AP rune, which is a popular choice for mages and for good reason. It's 4 times better than the equivalent glyph for some reason (normally quints are 3 times better). So if you want flat AP on your page, use the quints as the first choice rather than glpyhs.
Flat health is pretty poor value for its cost, but nowhere near as bad as the equivalent seal is, and it's better early on than some armour/magic resist is (which effectively add % to your health), so I can see why some people like them.
Well, there we go. Hope that was useful.
Let me know if I've missed out anything important.