I've been in JP just over a year now, formerly a resident of Allston/Brighton for nearly 10 years, and have not had much luck finding a great breakfast sandwich. I'm over near Forest Hills but would travel for a great sandwich. I used to eat egg & cheese sandwiches all the time, normally picking one up and running to catch the T. Would still like to!
So far my favorite is Java Jo's. Amazing sandwiches and food but tends to take awhile; i.e., give yourself 10-15 minutes per sandwich. Not ideal when you have a train or a bus to catch. Their sophisticated sausage is fantastic and is pictured with this post. I blogged about it here (http://www.fussy-eater.com/2008/10/java-jos-my-new-favorite-cafe.html). The newly updated and successfully moved Bella Luna has a decent breakfast sandwich too.
Interesting update. I've since sampled an egg and cheese sandwich on brioche at Bella Luna, which I thought was great and which my boyfriend loved. He said he wished he had ordered it instead! Nice endorsement. :)
Also I made it in to Ula's Cafe before 12pm (for once!) and they had these absolutely amazing ham, egg, and cheese danishes. I think they called them something else but I can't remember the name. I'm sure I probably ate almost a days worth of calories in that danish but it was worth every one - can't recommend this breakfast treat enough!