When a permanent phases out, it keeps all of its counters and enchantments and remembers everything about its previous life.
502.15h Phased-out cards "remember" their past histories and will return to play in the same state. They "remember" any counters they had on them, any choices made when they first came into play, and whether they were tapped or untapped when they left play. They also "remember" who controlled them when they phased out, although they may phase in under the control of a different player if a control effect with limited duration has expired.
Example: Diseased Vermin reads, in part, "At the beginning of your upkeep, Diseased Vermin deals X damage to target opponent previously dealt damage by it, where X is the number of infection counters on it." If Diseased Vermin phases out, it "remembers" how many counters it has and also which opponents it has previously damaged. When it phases back in, it will still be able to target those opponents with its upkeep-triggered ability.
When a permanent leaves play, it forgets everything about its former existence. It's not explicitly mentioned in the numbered rules, but the catch-all glossary has this:
Leaves Play
A permanent leaves play when it moves from the in-play zone to any other zone. See rule 410.10c. If a token leaves play, it ceases to exist. This is a state-based effect. If a card leaves play and later returns, it's treated as an entirely new permanent with no "memory" of anything from its former existence. (Phasing is an exception to this; see rule 502.15, "Phasing.")
EDIT: For Mikey's sake, you can definitely put his triggered ability on the stack and then respond by bouncing him with the Portal or whatever. The ability will resolve as normal and put -1/-1 counters on whatever creatures are in play.
(- Steve -)