I use 0.4mm for some prototyping when space is critical in the RF area, but I fab them myself, not sure if there are board houses offering this. CIF ABC16 which is also presensitised is what I use. In fact I only use CIF nowadays, too many inconsistencies with other boards to bother using them.
You are using CIF boards? Those are the worse crap I ever got. I binned the whole lot of it for the sake of my sanity. Some have a very thick layer of resist and others have an extremely thin layer. I got mine from Farnell BTW.
Anyway, I wouldn't use too thin substrates because the thinner the trace the more effect you'll have from etching tolerances. For self etching I'd certainly use 0.5mm as a minimum width if a trace needs to have a certain impedance.
Oh dear! I spent quite a long time battling with presensitised boards from Mega and others. I would often get regular streaking across the copper, almost as if it wasn't a uniform thickness either on the copper or on the photo stuff. I suspected my printer at one time. Almost as bad was that the way they were supplied, a dozen or so eurocard sized boards taped together, there were often scratches despite the plastic protection. The same seemed to apply to a few other boards.
Then by luck I used some CIF stuff because they had the thinner substrate for an RF project. I've never looked back, I always have stock of the 0.4, 0.8 and 1.6mm stuff (part numbers ABC16, ABB16 and AB16 respectively for double sided presensitised. It's the most consistent I've ever been able to do my own boards by a very long way. I can't remember the last time I had a board fail on me and I has to re do it (famous last words!) These boards are the sort of things I tack onto an order to make up the minimum order value.
I guess it's down to that magic sauce that you get when you finally have the process working. CIF was a part of it for me, although looking at others' experiences they seem to manage well with other methods. The toner transfer method for me was a failure, although I didn't try too hard. Truth is, I can get the chemicals out on the counter and have a board out and all packed away well within half an hour using the traditional photo method, down to 6mil track and gap if I push it, but usually I stick with the thickest I can get away with.
The boards I do are generally small, maximum maybe 5x5cm, for unit testing prototypes.
With the thinner boards, you do need to be very careful about flexing, they are not at all robust. This can lead to ceramic caps cracking almost invisibly, as well as making it a crap shoot with BGA type hidden pads if the board lacks coplanarity.
For vias, I drill 0.7mm holes and insert 0.4mm I/D copper rivets. For RF, I've got into the habit of putting them very frequently to stitch the upper and lower groundplanes. These are quite big vias, no good for production really, but for prototypes it's fine. Trying to drill much below 0.7mm at home is going to break a lot of drill bits even with a decent drill press.
Just me findings, YMMV of course.