Incantatrix is, along with Dweomerkeeper, considered by many to be the best Prestige Class. That said, there are many, many other great builds.
One main decision would be whether to focus or be versatile.
A focused build is centered on the idea that more of the same adds up -- have a look at focused conjurer specialists, for instance. At the end of the road are the single-spell builds who basically add up metamagic cost reducers to throw quickened, empowered, twinned, split ray enervations all day. Arguably incredibly powerful, one drawback of this strategy is that it can often be more easily caught off guard -- plus, it can get boring at times and feel like a one-trick pony.
A versatile build tries to accumulate different abilities to excel in diverse situations. Although Incantatrix and Dweomerkeeper are sometimes used for focused builds because of the sheer power they bring to the table, they make great versatile builds. One special subset of versatile builds is to build a character that combines the benefits of wizards with the sorcerer's flexibility -- mainly by using Prestige Classes (Mage of the Arcane Order), Feats and ACFs (Sponaneous Divination). Magic items nicely support this, too.
Everybody who enjoys playing arcane casters has his/her favourite builds. Some stick to similar concepts all the time, while others try radically different approaches. Personally, in a real campaign, I prefer to keep as many schools as I can. As most aspects of the game, this one really depends on the campaign, and the party, as well. I prefer a versatile spellcaster, because that is what the campaigns I play in demand. In a large group, as a secondary spellcaster, you might want to go a very focused road.
Some people have put a lot of work into these aspects and consolidated best practices into these guides which you might know:
Treantmonk's Guide to Wizards: Being a God
The Logicninja's Guide to Wizards: Being Batman
The Wizard's Handbook by Dictuum Mortem
While I disagree with all of the guides on some specific issues, there is great advice in all of them. If you want to plan a build and consider your building blocks, read all three of them, and then continue to the more specialized handbooks (conjurer's handbook, etc.).
