What are good general runes for tanking on let's say Alister, Rammus, and Shen.

I was thinking

HP Quints, Armor Marks, Dodge or MR Seals and CDR Glyphs. Will that be good?

Thats a good standard tank rune book.

Armor is also an option on Seals as is Magic Resistance on Glyphs.

I like armor penetration on Alistar for the early roaming damage, but Rammus and Shen benefit more from magic penetration as they mostly deal magic damage (Shen's passive is magic dont forget).

See this rune page guide for more info.

Why do you get flat MR glyphs over MR per level ones?

Here's my Tanky/Defensive Rune page.

Movement Speed Quints OR Flat Health Quints
Magic Penetration Marks OR Flat Magic Resist if I don't care about damage
Armor Per Level Seals
Magic Resist Per Level Glyphs

"Per level" resistance runes are so great. 24 MR and 24 Armor is pretty huge.

I also don't even bother with Dodge runes since it's near impossible to itemize for and only a couple champs really use it well.

Well I asked because it looks like on the Rune page they just do flat MR Glyphs but Per level Seals...

Runes that give flat bonuses are geared toward early game success. They're most often used by junglers and people who want to dominate the laning phase.

Ahh ok. That makes sense*. I usually play Ali or Rammus so my runes will be a little different. I think I would go CDR on Ali but max defense on Rammus