After having the same dilema (wanted a discrete install that I could have my phone standng up in) I came cross a post on a forum (cant remember where it was) that I developed bit. The guy had made a phone holder using hs ashtray. I have an Audi A3 and I know its possible with A3 / A4 because of the location of the ashtray, but it doesnt work on my mates BMW 3-series as there isnt enouh space for the iPhone to "stand up". Might work for you, depends on your car really.
What you need:
Your ashtray insert
30gb ipod dock insert (the little white plastic insert for the Apple generic dock's)
Dremmel (or similar)
Car bodyfiller (guess it would work with any type o filler but I prefer the car stuff)
Paint (to kinda math your car trim)
Its pretty simple to do. Cut a hole in the botom of your ashtray (and the recess in the dash) to pass the dock cable through. Glue the ipod insert into your ashtray so your phone sits the way you want it to. Once the glue dries fill and sand around the insert to leave you a smooth, flat finish with just the dock insert recess visible. Then paint the whole thing. Pass the dock cable behind the dash, up through the hole in the ashtray recess and glue into the "dock" you have made from your ashtray.
Couple of things you need to watch out for. The dock cable has the lock clips on the side (press the bottons to release the cable). The little metal clips on the dock need to be sanded back (I done this with the Dremmel) so the dock cable slips easily in and out of the phone without having to press the release buttons. Depending on the thickness of your ashtray, you might not get contact as the dock does not go far enough into the phone. Test this before glueing the cable in place (dont make the same mistake I did!!!). If its a problem, you simply sand back the plastic surround on the dock cable until the dock goes far enough through (2 or 3 mm should do it) or sand the bottom of the dock insert (or both as was the case with me!).
Thats about it really. I dont have step by step pics or anything (didnt think anyone else would be interested in this) but I if you want more info let me know - or I can get you pics of the finished job if you want.