Agreed, it can be hard to integrate other pieces of code into Moodle (By the way, Bob, ErfurtWiki is now completely integrated into Moodle 1.4 !)
I don't understand N's remark that ...
in a way Moodle's structure was now preventing me from implementing something that otherwise should be fairly easy to use.
If it has not (or not yet - look at the rate at which Moodle is developing) been turned into a Moodle module, it's always possible to install it as a completely seaparate application and then link to it from within Moodle, just like one would with a webpage resource. (as Bob suggested)
Of course the application will show that it's not a part of Moodle (theme / navigation / ...) but this would also be the case (I think) if one were to integrate it into one's own webspace: it would be just as difficult to make it look like the site's other pages. I don't understand the otherwise should be fairly easy to use part of N's remark. How can Moodle take away the ease of implementation of another application?
(N., I don't know anything about CSS and styles etc... I'm still using Moodle's original themes. Is that what you are referring to? Is Moodle's look making it more difficult to implement other applications without it being too obvious to the students using it...?)