Does Migration Assistant migrate macports?
The copying should work without a problem, but if you happen to upgrade to Snow Leopard at the same time, you might run into some compatibility issues, depending on the "ports" you have installed. Same goes for old "ports" that may have been specifically built for your old system (maybe processor dependent), you could run into problems there, too. 

Remember to run selfupdate, and upgrade the installed ports (where needed).