There's nothing wrong with using multiple storage engines on the same physical machine, as long as you understand the pros and cons of each. There are performance considerations, feature limitations and use cases for all the plugin storage types.
For instance, if you have a small table that's 90% writes, you might choose MyISAM. If the data can be regenerated easily and it's a small table, say for queuing, you might choose Memory. If you have a table that's 90% reads, and the data has got to be there when you look for it, then you'd probably choose a storage engine that supports transactions and configurable atomicity, such as InnoDB. If you want accessibility through the file system w/o damaging data, you might choose CSV.
Nonetheless, you can safely use multiple storage engines within the same schema as well as the physical host.
Let me note though, that your buffers play a role in this whole mess. If you use both MyISAM and InnoDB, you will need to be careful that your key_buffer and innodb_buffer_pool do not contend. This will take careful planning on your part, but that's what we do.