Taxxons: I try not to say "TAX-awnz" and go more for "TAX-ins", but it's gonna end up the first way anyway.
Hork-Bajir: "Hork-BAH-jurr"
Tobias: I know it's supposed to be "To-BYE-us", but I still think "TOE-bee-is".
Andalite: AN-duh-lite
Aximili-Esgarrouth-Isthill: Ax-i-MI-li-Ess-ga-ROWTH-Iss-thill
Elfangor: El-fang-or (with the "ng" sound kind of carrying over)
Escafil: ESS-kuh-fill
Helmacron: HELL-muh-crawn
Gedds: hard "g"
Yeerk: yee-urk, but more as one syllable. I just didn't want to type "yeeurk", because that's be a different pronunciation.
Visser: VISS-sir
Think that's all for the big ones. Now, smaller things:
Hereth illint: heh-RETH-i-LINT
... well, can't think of anymore.