Hardware

If you have large Innodb database size Memory is paramount. 16G-32G is the cost efficient value these days. From CPU standpoint 2*Dual Core CPUs seems to do very well, while with even just two Quad Core CPUs scalability issues can be observed on many workloads. Though this depends on the application a lot. The third is IO Subsystem - directly attached storage with plenty of spindles and RAID with battery backed up cache is a good bet. Typically you can get 6-8 hard drives in the standard case and often it is enough, while sometimes you may need more. Also note new 2.5″ SAS hard drives. They are tiny but often faster than bigger ones. RAID10 works well for data storage and for read-mostly cases when you still would like some redundancy RAID5 can work pretty well as well but beware of random writes to RAID5.

Operating System

First - run 64bit operating system. We still see people running 32bit Linux or 64bit capable boxes with plenty of memory. Do not do this. If using Linux setup LVM for database directory to get more efficient backup. EXT3 file system works OK in most cases, though if you’re running in particular roadblocks with it try XFS. You can use noatime and nodiratime options if you’re using innodb_file_per_table and a lot of tables though benefit of these is minor. Also make sure you wrestle OS so it would not swap out MySQL out of memory.

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