Keeping the dead... dead.

[Darkness]

It also suggests that the really evil need to be incarcerated rather than executed

I'd soul bind those, if possible. A prison demi-plane might be an option too. (A rapid-aging plane/demi-plane/whatever, if available, would be a viable execution method, come to think of it.)

Or, if you're evil (or even neutral, if you do it very rarely), turn them into undead.

 

[Taloras]

I believe that in one of the games i played in(for 2 sessions, epic levels, totally broken), we had a ghost with an aging touch. 10d10+10 years. Age the BBEG to the end of his natural life. Someone who dies from aging cant be ressurected.

 

[Elemental]

The psychic telepathy power Mind Seed is effective, too. The victim is still alive, they simply become a mental duplicate of you. It's instantateous (well, it takes a while to germinate once implanted, but the transformation is instantateous at the end of that duration), so it can't be reversed. Though it is the only psychic power with the Evil descriptor, if that's a problem.

 

[Storyteller01]

Do a remake of Edgar Allen Poe's 'The Cask of Amatillado'. Just make sure the manacles, mortar, and/or bricks are permenantly enchanted with Nondetection. Maybe supply a ring with the effect in place.

 

[Bihor]

There's a spell in Player's guide of Kalamar, call natural death.
Nineth level Cl spell.

 

[winterwolf]

Relics and Rituals (oh how I love the Relics and Rituals books) has a spell called Pass the Years (cleric or wizard 6th level spell) that ages the target 1d10 years (fortitude negates). While a low level party would have no chance to use this, a (much) higher group could. Also, a donation of 10000g to a temple would grant 15 castings of it (if you could find a temple with priests willing to do that) as each casting costs 660g (a 6th level spell cast by a lvl 11 cleric). Of course, the BBEG has to be alive to be affected by it...

 

[Thunderfoot]

1) Kill BBEG.
2) Bury body in CONSPICOUS location
3) Trap body with MANY spells of your choosing (Guard and Wards, Fire Traps, Glyph of Warding, Spellchains, etc)
4) Wait for allies to dig up body - go back and collect the treasure off the NEWLY MADE corpses of the BBGE allies.
Takes care of more than one problem - BBGE and his patsies.
Oh, defile the body - becuase its fun.

 

[NimrodvanHall]

kill your target with eneregy drain spells. undress him, cast soulbind on him, 3 times, to be shure he fails a save. donate the gem to the deity that hates him most.

or if powerfull enough kill him transform him into a skelton, and polymorph any object him into something wearable.

 

[HeavyG]

While you have his body, you might as well raise him yourself. It'll make him lose a level, unlike his allies' True Rez and will make his allies waste super-valuable spell components.

Then keep him drugged up in a dank cell somewhere. Maybe set a trap for his allies or cast Mind Blank on him.

Or, if evil (or pragmatic-neutral), you can always kill him again and repeat until he's first level. Then send him back to his allies.

Does Restoration restore lost levels due to raise dead ?

 

[Chorn]

While you have his body, you might as well raise him yourself. It'll make him lose a level,

Once again, as Tatsukun pointed out earlier, resurrection magic won't work unless the subject is willing to come back. All of them let the target know the identity of the caster so the BBEG will refuse any attempts not made by someone he does not know.

Does Restoration restore lost levels due to raise dead ?

Negative. The Con or level loss from being raised cannot be restored by any means. Check the relevant spell descriptions and you'll find a line in every one of them stating such.