Depend agains who you're going and what champion you pick.
MR runes are very important to survival in the lane (keep in mind that you want to stay as long as possible in the lane and farming/leveling), and usually you're going against another Magic User (ap). Glyphs are the way to go in those runes
Armor runes are also important in the lane for survival, the minions may kill you if you keep receiving damage (usually when you go after your opponent and go behind the enemy minions, the minions will turn up on you). These runes also help a little in late game. Seals are amazing for those runes.
Armor Pen. runes are not so much of use, if you are going as Fizz. They are great if you are Vayne for example. But if you want those (as Vayne for example) go for Marks and/or Quintessence
Magic Pen. runes are great for you, in early, mid and end game. Marks are usually enough, but you can get some Quintessence too.
Hybrid Penetration. runes are excellent on Fizz in the early game, but in the end game, you main damage will be upon the magic damage, since you'll hardly be able to do 3 hits in a row against a target (usually, you'll just jump, pop the ultimate, then scape from the mess, while your team finish the opponents and the opponents try to kill you). In the early game, if you are aggressive, you'll be able to jump in behind the minions, hit once or twice each "dive" then retreat. The main point on the Armor pen is the damage on the minions.
It's always worth to test YOUR play-style, and pay attention to:
- Do you keep receiving minion damage on your engages?
- Do you wait until 6 to start Harassment? or you go for it since level 1?
- Against who you usually play? (do you go for matches that you know who you are going against or it's a "blind date"?
Based on that, you can pick your runes and also, if you want them to be Flat or Scalable.
- Flat before 6 usually.
- Scalable after 6 usually
There isn't a "best-rune-set" nor anything like that. But the set of runes that Valentin Grégoire said in his answer, is a good way:
- Flat MR Glyphs (blue) x9
- Flat Armor Seals (yellow) x9
- AP or Magic Pen Marks (red) x 9
- AP or Magic Pen Quints x 3 (or put some movement speed in there).