I've seen not properly aliened text and controls in the linux version.
I think that modern programs should not feature fixed sized dialogs, etc. Modern programs should be more like a good web page.
Other problems that occur not only in open source programs but in commercial is that when translating a program into another language: sometimes the text doesn't fit at all.
original
-> Properties
but
-> Einstellungen
-> Настройки
original
-> Dialog window
-> Dialogfenster
but
-> Диалогов прозорец
Some languages are more descriptive than other and need longer or more words to describe something than English.
Also in my oppinion when properly designed tab based iterfaces look better than dialog ones and are more natural. For examples the Settings in CB are "tab based". But I believe most of a program could be designed like that. One big window and tabs inside (MDI). Why is it better than Dialogs - because most of the time, when you pop-up a dialog, you can't use the main program anyway. Pop-ups, message boxes, dialogs, etc. should be reserved for the most important stuff only and some designers used/abuse them for anything.