Good feedback so far guys. This stuff really helps. Coming from a thick client background means I know a lot about the languages and principles, but there are some concepts I've still got so much to learn about in the world of web programming.

So far it sounds like my concerns are probably valid, though perhaps not my first guess at a solution. To that end, how would you handle the problem? To state it specifically: there are huge chunks of JavaScript in the common files where the code has to distinguish between appications in order to function properly. This is difficult to maintain and has (along with good dose of non-testing) resulted with applications in production being broken due to changes made in other applications.

An example of this is
if thisapp ...
else if thatapp ...
else if someotherapp ...
repeate a few dozen times.

Then do it again for various functions. This goes on for about 3000 lines of JavaScript in one instance all to draw the correct options on a toolbar.

Now normally in the thick client world I would create a class for the generic behavor and then seperate classes for each app so that code is grouped together logically. That would keep people from messing with the main base file all the time and blowing up other applications (which is happening). In the toolbar example you'd have a generic object that can contain buttons and might even have a few generic ones (close, load document), but each inherited toolbar could then add whatever buttons safely without affecting any of the other applications' toolbars. I know this could be done by moving all of the code server side, but are there other options or things to think about?

Thanks again in advance. With a little more help I might actually sound intelligent when I make my recommendataions on all this!