There are a variety of different ways of encoding information in a normal transaction in the block chain.
Encoding the information as fractional amounts of bitcoin in transactions has several disadvantages.
It is inefficient - the amount of information encoded per transaction is small.
It is obvious - small transactions which are not round amounts of coin are not typical.
It can be discouraged by fees on small untypical transactions.
Another way would be to send a small amount of bitcoin to an address, were the address is the information to be encoded. This would store about 20 bytes per transaction.
A superior way would be to use the broadband subchannel in ECDSA which I wrote about in http://bitcointalk.org/index.php?topic=1545.msg18364#msg18364
This allows you to store 32 bytes per transaction and does not require you to waste any money.
Neither of these latter two schemes is obvious, nor can they be discouraged by fees and they are vastly more efficient.