Crucible Marks are obtained by anything and everything PvP. The amount you get varies on performance and game mode.
Vanguard Marks you get by doing the Strike playlist (opens at around level 17). You can also gain marks at a much slower rate by doing other PvE interactions, like patrolling and random events that appear during patrols. The amount you get varies on the Strike Difficulty selection you chose.
Both kinds of Marks have a weekly earn limit of 100 before you can gain more again. The time renews on Tuesdays, IIRC.
NOTE! This answer was accurate(-ish) when it was posted but recent patches have changed a lot of the things posted here. Please seek out updated sources of this information!
Glimmer
Earned by:
- Killing majors or ultras (mobs with yellow health bars)
- Dismantling gear (weapons or armor)
- Reward from Cryptarch from turning in items you pick up during missions (House Banners from Fallen, etc.)
- You can use an item corresponding to the type of mob you're killing and get extra glimmer from every mob killed for a short period of time (10 minutes)
- Completing missions
- Completing PvP sessions
- Opening random chests
Spent on:
- Buying items from various vendors in the tower, including weapons and armor, replenishment items, emblems, etc.
- Upgrading gear (some upgrade slots require glimmer, others require glimmer + items)
Destinypedia: Glimmer
Vanguard Marks
Note: You need to be level 18 or higher before you start earning these.
Earned by:
- Completing public events
- Completing strike missions
- Completing your first public event each day (gives 2)
Spent on:
- Buying gear from some vendors in the tower, level 20 legendaries, ground vehicles, etc.
Note: You can only earn a maximum of 100 between weekly resets (Tuesdays, 9am UTC if I'm not mistaken).
Destinypedia - Vanguard Marks
Crucible Marks
Note: You need to be level 18 or higher before you start earning these.
Earned by:
Spent on:
- Buying gear from the crucible vendors in the tower, level 20 legendaries, ground vehicles, emblems, etc.
Note: You can only earn a maximum of 100 between weekly resets (Tuesdays, 9am UTC if I'm not mistaken).
Destinypedia - Crucible Marks
Strange Coins
Earned by:
- Dismantling legendary or exotic gear (random)
- Mission rewards (random)
- PvP rewards (random)
- Weekly heroic strike mission (minimum 3, maximum 9)
- You can do it at level 22 (which gives 3 coins), level 26 (which gives 6), or level 28 which gives 9.
- If you first complete it at a lower tier (level 22 or 26), and then complete it at a higher tier (26 or 29), you get awarded the difference. Example, you first complete it at level 22, giving you 3 coins. If you then complete it again at level 26 or 28, you will get 3 or 6 additional coins, respectively. If you first complete it at the highest level, you will not get strange coins from repeating it at any level the same week.
- Weekly nightfall strike (random amount)
- Opening chests (random)
- Public events (random, but requires gold tier participation)
- Decrypting engrams (random)
Spent on:
- Buying exotic gear from Xûr
Destinypedia - Strange Coin
Motes of Light
Earned by:
- You get one at level 20
- When you earn experience after having already reached level 20, you earn xp towards a new mote of light. You can check the level tooltip in the game to see your XP progression towards the next mote of light
- Opening chests (random)
- Mission rewards (random)
- PvP rewards (random)
- Decrypting engrams (random)
Spent on:
- Buying exotic gear from Xûr
- Class items and emblems from the Speaker
Destinypedia - Mote of Light
As for "what is the best", at level 20 your main goal will be motes of light and strange goins as they will allow you to purchase exoting items with Xûr. Note that he only arrives during the weekend (Friday 9am UTC - Sunday 9am UTC, give or take a few minutes), and his inventory is random and doesn't refresh until next week, so you may or may not actually find anything useful on him
Second to that you have Vanguard or Crucible marks, which will allow you to purchase legendary items from the Vanguard and Crucible vendors.
These things are predictable in the sense that you can pick what to do depending on what kind of currency you want, to a certain degree.
Best Answer
Legendary marks can be earned in a variety of ways.
To my knowledge, the Nightfall strike itself does not reward any marks.
As noted, Heroic Strikes, Daily and Weekly Crucible are all per account.