A needs line of effect to every space into which a spell will create an effect
The Player's Handbook on Line of Effect, in part, says, "You must have a clear line of effect… to any space in which you wish to create an effect" (176). Further, on Effect says
You must designate the location where these things are to appear, either by seeing it or defining it (for example, "The insect plague [effect] will appear 20 feet into the area of darkness that the nagas are hiding in"). Range determines how far away an effect can appear, but if the effect is mobile (a summoned monster, for instance), it can move regardless of the spell’s range." (175 and link mine)
Further, special rules apply to effects brought forth by spells of the magic school conjuration:
A creature or object brought into being or transported to your location by a conjuration spell cannot appear inside another creature or object, nor can it appear floating in an empty space. It must arrive in an open location on a surface capable of supporting it. (172)
(It's a mystery to this reader why the printed text presents this information in exactly the opposite order that the reader needs it!)
A spell of the subschool summoning typically creates an effect, so the caster needs line of effect to the entire space into which the summoned creature or object will appear. Likewise, a caster needs line of effect to the entire space where a wall spell—like the 6th-level Sor/Wiz spell wall of iron [conj] (PH 299)—will see its effect created. Finally, a caster needs line of effect to the entire space where a sphere spell—like the 4th-level Sor/Wiz spell Otiluke's resilient sphere [evoc] (PH 258)—will see its effect created.
Finally, the Player's Handbook on Line of Effect also says, "An otherwise solid barrier with a hole of at least 1 square foot through it does not block a spell's line of effect" (176). A 6-ft. diameter pillar occupies the square it's in and some of the surrounding squares, so it's a barrier and would prevent the creation of effect spells in that the square it wholly occupies. However, in the surrounding squares—into which the pillar's diameter extends only 6" or so—there is much more than a square foot into which to put stuff, and it wouldn't block line of effect. (By the way, a pillar in D&D 3.5 is usually either slender—not occupying a square therefore not a barrier—or wide—occupying a square therefore a barrier.)
Some sphere spells—like the 9th-level Sor/Wiz spell prismatic sphere [abjur] (PH 264)—are given Effect entries the DM should probably modify these spells.
That is, when such a spell tries to create an effect that's a sphere around a creature and that sphere effect would extend beyond the creature, such a sphere spell should create an effect that's a dome over a creature that's on a surface, the remainder of the spell's effect occluded by the surface. However, a spell that creates an effect that's a big enough sphere—like the prismatic sphere spell's 10-ft.-radius one—means that unless the caster somehow has line of effect to the space beneath the target the spell should, instead, technically fail as the caster doesn't have clear line of effect to those spaces because those spaces themselves aren't clear.
The Player's Handbook on Spell Failure says
If you ever try to cast a spell in conditions where the characteristics
of the spell (range, area, or the like) cannot be made to conform, the
casting fails and the spell is wasted. (171)
And a spell like prismatic sphere doesn't allow any choices when its effect is created. For example, the spell wall of iron has Effect: Iron wall whose area is up to one 5-ft. square/level, but a prismatic sphere spell has Effect: 10-ft.-radius sphere centered on you, without an up to and without any concessions for creating an effect at anything less than its maximum—and only—size.
In sum, by a strict reading, such a spell can affect only a creature that's flying, swimming, and the like. To avoid pointlessly penalizing such spells and having archmages looking like nitwits because they forgot this technicality, this DM recommends changing such spells on a case-by-case basis when appropriate, and, as always, the DM first informing players of this change.