Let's see...
Due to the double-save, the Shadow line of spells is mostly useful when you can do one of:
1) Pump the DC to insane levels, so it doesn't matter that they get two saves
2) When you can use them in such a way that the save doesn't matter (anything where you're casting it on yourself, essentially, but also if you're just using it for flanking).
3) When you can avoid expensive components, and spam the effect.
Case one should be pretty obvious - if they don't save, it has full effect on them.
Case 2 is slightly less obvious. For instance, Greater Shadow Evocation can duplicate Contingency - and as you can give up the save, you have full chance of it affecting you - so the Dimension Door works every time. The regular Shadow Conjuration can duplicate Phantom Steed - and as you can voluntarily fail a save, it's just as effective as a regular Phantom Steed, except for the hit points. Further, if the only purpose of the shadow-creature is flanking, then the save doesn't matter (it still threatens, even if it does a lot less damage), so the standard-action disposable flanker for the Rogue of the party is very handy. Technically, Shades can duplicate Greater Teleport, Greater Planar Binding, or Draconic Ally (Spell Compendium) - but that's more likely an oversight than anything else, and many DM's (not all) will impose the subschool restrictions from the lower-level versions of the spell to Shades.
Case 3 is an odd one. Sepia Snake Sigil is a Conjuration(Creation) spell - so it can be duplicated. However, Shadow Conjuration (and company) don't inherit the components line - which means it's free. Ditto for a Shades Magnificent Mansion (no focus), and so on. It also means that if you somehow get separated from your component pouch, you can still cast stuff.