My advice is to allow the Spell Compendium only as a source of spells that the wizard may research. Treat them all as uncommon or rare spells that can' t be chosen as part of the 2 free spells per level. Since none of the NPCs in the adventures use these spells, you will need to choose new spells from the book if you open it up to the PCs.
As for nonstandard classes, I don't see too much problem with classes like the knight. It may even help a budding Knight of Solamnia out at low levels. I strongly encourage picking up Knightly Orders if you are going to have any knight characters however, as it revises and updates the Solamnic and Legion PrCs and introduces some new feats that are good choices. Towers of High Sorcery revised the Wizard of High Sorcery, also, relaxing some of the entry requirements and adding new PrCs, spells, and items that are used in the campaign in places.
Other than those two books, you may also want a copy of the Bestiary of Krynn. A revised edition of that book will go on sale around April, but is already on sale in PDF form at DriveThruRPG.com.