For the first time ever in NWN, I have reached the epic levels. My character was a Wizard 13 / Rogue 2 / Arcane Archer 5.

Now I have to choose what the level up in, but also what feat to choose from.

I think I have narrowed down the feats to:
1) Greater Spell Penetration (spell resistance is the number one biggest pain in the butt to a spellcaster - does this feat make a noticeable difference?
2) Epic Dexterity - to improve my Arcane Archer even further
3) Epic Intelligence - to improve my Wizard even further
4) Epic Toughness - more HP equals living longer
5) Maximise Spell - I only have a couple of Empowered Spells memorised so not sure how much use I would get out of maximised versions.

Any thoughts?

Epic Toughness isn't that good - it's worse than normal toughness.

I'd suggest Epic Weapon Focus, Great Dexterity or Great Intelligence - and Epic Dodge is a GREAT feat, for further levels.

How much use would Greater Spell Penetration be? Every monster I encounter seems to have Spell Resistance now, which kind of nullifies the whole point of having offensive spells at all.

Your wizard levels are too low. Beating spell resistance (the max a creture can get is 32) is based on the caster level:
Caster Level + 1d20 + spell penetration feats.
If you want to play an offensive caster - but it's a bit late for this build - the Great Intelligence and Spell penetration are good choices.

Unless wizard is the only class you'll take levels in from now on, GSP is a waste. As Chimera said, your caster level is simply too low. Great [attribute] feats are always a solid choice, as is epic prowess, epic spell focus. Blinding speed is completely useless in OC.

Just about any other epic feat tree requires a high physical stat. Strenght for dev crit string of feats, dex for self concealment, epic dodge and blinding speed and Con for damage reduction.
You probably dont have either in extreme, so you're free to go wherever you wish.

Hmm, thanks for the explanation of how spell resistance worked. I never understood that before.