Quick review of a few choice favorites for a ton of people.
Invisible Spell: Hands-down one of the most versatile, though with some slightly puzzling applications (Invisible Invisibility, anyone?). Get around the most troublesome problem with BC - making your enemies fall for your traps!
Cooperative Spell: Big on NPCs, subpar on PCs (unless we're talking someone with Simulacrum as a SLA).
Energy Substitution: More often than not it's either for prerequisites or for specialized builds (often centered on Searing Spell, Born of Three Thunders, etc.) or with PrCs that grant you benefits when using spells of certain elements. Pick Sonic and you will find practically no resistance, ever.
Lord of the Uttercold: Specialized? Yes. Awesome? Also yes. Combine with Piercing Cold and/or Fell Drain for a nice and effective combination.
Nonlethal Substitution: Are you exalted? Cuz if you aren't, you probably got no use for this one.
Sanctum Spell: Most useful for early qualification shenanigans.
'Sudden' metamagics: Most useful on one-shot, low-level campaigns, or when you expect retraining further down the road - otherwise not worth it.
Extend Spell: Not only is it a prerequisite for Persistent Spell, it's also pretty good on its own, specially when applied to spells with an hour/level duration.
Fiery Spell: Even on a specialized build, this is probably unecessary.
Piercing Cold: Special PrC note: Winterhaunt of Yborighu. You get to freeze people to death at no adjustment!
Retributive Spell: Could have some interesting applications, but as a general rule you should avoid getting hit at all costs. Wizards make for lousy masochists, after all.
Sculpt Spell: a Battlefield Controller's best friend. Particularly useful in spells with small areas.
Searing Spell: Piercing Cold, baking version.
Silent Spell/Still Spell: Still is more useful than Silent in a great deal of cases. Use both and you will not seem to be casting a spell at all. There's a skill trick that can replicate this latter use, but only with Silent do you get to cast in a zone of silence. Still Spell is also great in conjunction with teleportation spells for a quick getaway when grappled.
Transdimensional Spell: Nice if you're facing incorporeal targets all the time. Otherwise, stick to Force spells.
Empower Spell: Mathematically superior to Maximize Spell. Dirt cheap for its effect too.
Fell Drain: Kewl on a necromancer. Shivering Touch and Parching Touch are particularly nasty candidates.
Ocular Spell: Persist shenanigans ahoy! Makes a lot of awesome spells persistable.
Reach Spell: Similarly nice, like Ocular Spell.
Split Ray: Exceedingly nice for its cost. Twin it for maximum fun!
Chain Spell: Good for A) eliminating mooks and B) no save debuffs. Chained, Reached Shivering Touch. Sounds good? It's best used on spells whose effects either rely on damage for happening or that screw the target over regardless of saves (Hello Enervation! How are you?)
Fell Animate: Cheap way to get cannon fodder. It's basically a low level undead creation spell with no cost for materials that you attach to another spell. Regardless of who you target this with, the zombies will probably be useless to deal any real damage, unless you can buff them to ridiculous proportions somehow.
Widen Spell: It's essentially best applied either to spells with a large area to begin with or buffs that work over an area rather than several targets. One of the Battlefield Controller's best friends.
Repeat Spell: This one can be difficult to use. Since the targets must be the same and the battlefield is often in constant flux, it has limited applications. One thought, however: Repeat Spell + Delay Spell (Consumptive Field).
Energy Admixture: Very expensive for its effect. I suppose there ARE some combinations that could make this worth it, but overall there are better ways to increase damage output.
Quicken Spell: saving up actions can be crucial during combat. According to the PHB II, quickened spells cost swift actions instead, so it's better used on spells with a casting time longer than one standard action.
Twin Spell: It's there if you need it. Best used with spells with cumulative effects (namely damage or healing) or that provide cumulative penalties (such as enervation). Its high cost makes regular uses impractical unless you can reduce or waive them somehow. Where blasting is concerned, its combination with Split Ray is difficult to beat.
Persistant Spell: Very, very powerful, even considering its cost. While inexpensive to obtain, proper application of it can easily break otherwise perfectly balanced spells. One of its most infamous uses: Persistant Delay Death. Due to its limitations, best applied (exclusively?) to buffs.