1. With strange consequences.
2. With patience.
3. With difficulty.
4. With your fingers pinching your nose.

1. with medieval noodles!
2. with perplexed ladder!
3. with unrecognizable atomic borders!
4. with pin!

Pit them against one another. Pit Superman with reality warper and let the reality warper render his power useless. Kill them both with snipers. Reality warper can warp reality but they can't read the future so a sudden shot to the head suffice.

Now with time master and eldritch abomination it getting a tad bit complicated. Sure you can pit them but you need to plan ahead. Like.... a couple generations ahead. Time master will surely kill the eldritch abomination but you make sure to trap the Doctor on a place he can't react quickly. Also FFS kill him quickly, most Doctor's enemies took their sweet time to kill him and ended up failing. A sudden death always give us good advantage.

Regeneration? **** that. You ask me to kill him once. After I killed him I just GTFO from there and hope he doesn't remember who killed him.