At the dealer... a lot. If you go to a local bmw mechanic it won't be too back.
Spark plug change... $50 max, parts are only about $15.
Water pump and gaskets etc will be around $200.
Brake flush you can do youself... if not, $50-60
Fuel system.... maybe $50-75
They don't need tuning... vanos tunes itself.
My personal advice.... buy a book called "101 performance projects for your BMW 3 series". Do it all yourself... learn a lot... save a lot... and if you do it yourself, you don't have to worry about mechanics taking any short cuts.
I have learned everything on that list from the book. I haven't done the water pump or fuel filter though. But I know how to from the book.
You can also buy your own parts from bavauto.com to prevent mechanics from trying to rip you on the parts.... and they might not be trying to... but their prices are higher than bav's.
PS... the 90K mile service is A LOT... I have never paid anyone to do it. Look in the back of your owners manual, it tells you everything they check. I check it all myself. If you change your own oil scope things out while your under the car. It's easy to spot stuff that is wearing out. You can reset the service light yourself too.
If you don't know anything about cars however.... don't try doing it yourself.... in other words... if you are scared of doing it, don't... if you feel confident... go for it.
Also... the first time you do things it might take an hour... second time will take 30 mins... 3rd time you do something it will take 10-15 mins. Most of the projects I have done have been like that. From rebuilding the internal door mechanisms to working on the engine... that's how it's been for me. Key is to not let yourself get frustrated.
