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MySQL Blog:: Innodb or MyISAM? What's your preference?
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For reliability and performance, we use InnoDB for almost everything at Wikipedia - we just can't afford the downtime implied by MyISAM use and check table for 400GB of data when we get a crash.
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The speed advantage of MyISAM is overstated IMO. LiveJournal with a mostly write environment saw a big increase in speed when it switched from MyISAM to InnoDB and they are very happy with InnoDB.
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MySQL Engines: MyISAM vs. InnoDB | Tag1 Consulting, Inc.
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A database layout with most tables being InnoDB (for performance and data security) and the search tables being MyISAM (for performance on that particular workload and acknowledging the fact that, if that data was corrupted, it could be easily rebuilt) is an excellent fit.
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It is important to not run at 100% usage of the innodb buffer, as this likely means that you're not buffering as much as you could for reads, and that you're starving your write buffer which also lives in the same global innodb_buffer.
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