I basically play flat armor seals and swap them for flat health seals if I'm playing in mid against an AP mid or as a supp with armor quints. Scaling health is usually too much of an early drawback to pick up. But the health runes threshold is level six (the point where scaling ones get as strong as flat ones). So you can use them whenever you think you'll be safe pre6 if that's your personal preference.
Armor is pretty much always viable, flat HP can just be a bit better early. If you don't want to buy those HP seals for 810g x9, you can well go with just flat armors. I've played accounts into plat and gold without getting any other seals than flat armor, they're almost always okay.
Check out this quick overview of runes played by the pros in the MSI to get an idea:
http://euw.leagueoflegends.com/en/news/esports/esports-editorial/check-out-our-handy-msi-rune-guides
They also pick up HP on supps and against AP matchups and otherwise go for armor.
Flat Armor Seals:
- the opponent laner is in some way autoattack based
OR you are jungling
OR you are playing adc
OR you are playing top in a blind pick (as it's likely they'll be normal damage based in a way)
> Flat armors are the basic option. You can run them anywhere and always.
Flat Health Seals:
- if you are up against a champ that almost only applies magic damage like that mid lane Karthus
OR if you are supporting and you've already got armor in your quintessences
- especially on mid laners due to the shorter lane (you'll rather need to survive burst on ganks than sustained normal damage) and the many AP carrys
- especially against Ignite opponents as the true damage is flat and not a percentage of your HP and you'll withstand bursts better
Scaling Health Seals:
- basically unnecessary ; you can however pick them:
- if you're really confident in a lane -> to get that extra advantage later on when you dominate early anyway
- if you're playing a playstyle on your champ that focuses on building up a strong late game, like a mid that scales very well or a Nasus in an easy matchup or something
- if you are building armor and mresi anyway, especially stuff like Frozen Heart that lacks HP in itself. Similar to a shield, health will be more effective then as it drops slower.
- if it has interscalings aswell: your champ has skills scaling with health, a Braum Q, Volibear W, Shen Q, Taric Q or something like that.