this is pretty straightforward, not too technical though:

http://forums.devarticles.com/general-sql-development-47/difference-between-myisam-and-non-myisam-tables-1745.html

FTA:
"MyISAM is of course the default table type i'm MySQL. It's
an improvement over the now-deprecated ISAM table type. It
provides a simple tree structure for quick indexing on small
tables, typicall fewer than 10,000 rows of data.

There are some other types of tables supported in MySQL,
most of which won't provide any noticable differences.

A MERGE table is a table that only exists in memory, and
will not be saved if MySQL crashes or has to be restarted.
It is, as the name suggests, a merge of two (or more)
tables. If you drop a MERGE table, it only drops the
reference to the merge, not to the tables that are combined
in it. It's not good for much!

Another table, the one which is best for huge tables, is
InnoDB. It's probably the best RDBMS out there; it's
actually a whole set of drivers on it's own, and when you
use it, MySQL is really just a wrapper around the InnoDB
table. Slashdot and other megamammoth sites out there use
it, it's fast and effecient, but the trees are pretty large,
so it's not good for smaller tables.

There are a few others.. like BerkeleyDB, which isn't
anything special and doesn't provide any major performance
increase.

The major difference between the various table types are the
data tree structures and how they're handled within the RDBMS.

In the end, you'll probably find yourself sticking to MyISAM
unless you're on a very large-scale project, in which cas
eyou probably woudln't use MySQL anyway =D"

There is foolowing Differences between MYISAM and InnoDB
ENGINE:-

1)MYISAM does not support the foreign key constraint and
transaction but InnoDB support it.

2)MYISAM is faster then the InnoDB but in case of perforing
the count operation it takes more time then the InnoDB.

3) MYISAM occupies less memory sapce for tables rather than
InnoDB tables.

1.Transactions:MYISAM doesnt support any database  
transactions means if the transactions related to large 
amount of data transfer it will not provide because memory 
is less. But INNODB will provide transactions.

2.Locking:MYISAM provide the table level locking means if 
the data in one table has been modified by the other 
table ,the entire table will lock for the next process.But 
INNODB provide the row level locking only the row of the 
table that is being updated is locked.

3.Foreign keys – MYISAM tables do not support foreign keys. 

4.Data Types:MYISAM provide a full variety of datatypes,but 
INNODB will not.

MyIsam provide full text search which is not supported by 
Innodb

innodb is acid engine

it supports online backups

innoodb has maximum performance for large databases

myisam supports table level locking where as innoodb
supports only row level locking when updated