Kopachris: There's about 20 waves of Thoths before they run out, and I've never managed to get anywhere near killing them all. Unlike Nahemas, which are incredibly slow and thus sitting ducks, Thoths actually fight and are fast and maneouverable enough to get behind you pretty quick.
My wingmen in this mission almost always die before Delta Wing becomes available, regardless of what fighters they're flying. The reason I put them in Hercs is because they have a lot of firepower, so I can order them to destroy the Thoth's Weapon's subsystem before Delta wing arrives, which improves everyone's survivability all around. Delta wing is always in Valkyries, I don't have a choice in that matter.
At about that point the Thoths arrive, and the rest of Alpha wing almost always gets trashed - if I go after one wing of Thoths, the other one murders the rest of Alpha wing before I can get to them. If I'm the only one fighting them, and I'm trying to actively kill them, then my chances are almost nil - they outnumber me six to one, and there's no way for me to target one without having three or four of them shooting me from behind at the same time. Charging straight at a group is suicide too, since they shoot at you with Interceptor missiles - if you're flying a Herc, then one frontal hit from an Interceptor causes hull damage, even if your shields are completely full (the fact that this doesn't happen with a Ulysses, and because the Ulysses is maneuverable and fast enough to easily dodge the missiles is why I like to fly the Ulysses).
Delta wing tends to survive because once Epsilon 1 leaves with the Giordano and all of Alpha wing other me is destroyed, the Thoths tend to want to kill me, rather than Delta wing. This means that I can distract the Thoths and play cat-and-mouse amongst the Typhon while Delta does most of the damage, with me ordering them to destroy any turrets as I dodge away. The Thoths inadvertantly help me out by shooting the Thyphon every time they miss my ship.
Once the Typhon is ready to blow I pump all my power into my Engines and afterburner out of there. As I'm making my escape, I order Delta wing to cover me - since the Thoths inevitably all come after me, they get wasted by Delta coming up from behind them.
It's not actually that hard to pull off now that the Typhon is no longer invulnerable.
Mars: I just don't bother with the Thoths until the Typhon's gone - its MUCH easier that way. Also, I've actually not flown the Apollo at ALL since the Hercules and Ulysses became available. The Hercules has more firepower, and other than having slightly less missiles, the Ulysses is superior (better maneuverability and shields). I can run rings around most enemies with the Ulysses, which makes it one of my favourite ships.
Clawandfang: While I certainly have played and do like Legacy of Kain, my screenname isn't from the series at all. I've been using 'Soul Reaver' as my online name since before the first Blood Omen game even came out, so I can assure you it's not from there. It's actually a name of a character I created... he's one of the main characters in a single player Warcraft III mod I'm making... the first five Chapters have been released already, and I'm working on Chapter VI at the moment (official site's at www.familykrieg.com/tothebitterend
in case you've got Warcraft III:TFT and would like to give it a shot)