If I added all the maps included in packs (like for example all the qte*m* maps in Travail) to the list of possible startmaps, how should they be shown?

a) Alphabetically:
e1m1
e1m2
...
e1m7
e1m8

b) In order of appearance (this would be nicer for non alphanumerically ordered ones):
...
e1m4
e1m8
e1m5
...

Should secret levels be shown?
Should the level names (not only the filenames) also be shown (please no, too much work)?
Should the Injector remember the currently selected map?

I plan to add a "continue from last savegame" feature so that last idea might be absolutely unneeded. 

Also, is anyone apart from megaman and me testing recent git versions? Are there any mean bugs that we are unaware of? 

Here's the list of bugs that we are aware of (and that aren't already fixed in the git releases):

http://github.com/hrehfeld/QuakeInjector/issues

Feel free to add bugs and feature requests, or maybe just details for existing ones. 

i'd show the levels in alphabetical order. For cases where the order is not the same as the "play order", i think that is intentional on the part of the authors. e.g. the name "e1m8" doesn't give you any hints about what level the entrance is hidden in, but if you put it after e1m4 in the list, then it does give a hint. 

Well done!