Here's my experience.
The main problem with setting up new front speakers is that the factory mounts are very shallow so most speakers wont fit without heavy modifying and/or cutting the door panel.
The second problem is that the speakers are mounted to the door cover panel and not the actual door. Which means that your bass will always suffer.
The proper way to go would be to cut speaker size holes in the door and re-do the cover panel for proper mounts. But that seemed like too much hassle to me
So I decided to go with factory mounts.
The not all standard speakers (6.5") will fit, they need to be low profile if you want to fit them in the factory slot.
In my case I used old MB Quart PSD 216 midbass. I dont think they make them anymore. You can also go for Rainbows they have custom built model for e46, heard good things about them.
I also used two mounting rings per midbass, something like this http://i.ebayimg.com/00/s/MTAwMFgxMDAw/z/AswAAOxy6MBSSqMj/$T2eC16dHJGIFFonMC7myBSSqMi5Yn!~~60_57.JPG
Covered the door panel inside out with dynamat, also added around and on the mounting rings.
Morel MT12 tweeters went in to factory slot instead of the stock ones.
New wiring, no filtering (HU takes care of that)
The front is driven by Audison LRx 4.5 one channel per speaker

In the boot on the battery I have a Hertz hx250d in a custom made sealed box (made it ages ago so dont remember capacity, ~25l I think).
This is driven by Magnat tribal X One.

HU at the moment is CDA-9887 but this is in the process of upgrading to 7" Android tablet.
Will do pictures on this once all the parts arrive.