Here are just a few that come immediately to mind.  There may be additional differences as well.

• Although it is generally best not to do so, it is possible to spend unconfirmed bitcoins.  It is not typically possible to spend the money from an uncleared check.
• It is quite easy to see in advance if it is extremely likely that an unconfirmed transaction will confirm.  It is typically very difficult to determine ahead of time if a check will clear.
• It is relatively easy for the sender to remove funds from an account before a check clears, while it is quite difficult to successfully double-spend a properly formed bitcoin transaction
• The properly formed bitcoin transaction will typically (more often than half the time) confirm in less than 10 minutes and rarely (if ever) take more than 120 minutes, while the uncleared check will take days to clear

A properly formed bitcoin transaction is much more analogous to a credit card transaction that has received approval from the processing company and has a valid looking signature on the receipt than to a check in the mail.