If a Ruin Runner is on the board, and my opponent plays a Thousand Tailed Watcher, does the Ruined Runner get -3 might?

Yes, Ruin Runner will receive the -3 Might reduction from Thousand-Tailed Watcher.

The reason for this interaction is that Thousand-Tailed Watcher's ability does not choose (target) specific units; it applies a global effect to all enemy units. Ruin Runner's ability states, "I can't be chosen by enemy spells and abilities," which only protects it from effects that require a player to specifically target it. Because the Watcher's ability affects the entire board without targeting, Ruin Runner is affected normally.

Key Details:

• Targeting: Because the Watcher's ability doesn't use the word "choose" or "target" for the units it affects, it bypasses Ruin Runner's protection.
• Minimum Might: Per the text of Thousand-Tailed Watcher, Ruin Runner's Might will be reduced from 5 to 2 (it cannot be reduced below 1).
• Timing: This reduction only applies to units already on the board when Thousand-Tailed Watcher's "When you play me" ability resolves.