As my car is 20 years old and a daily driver I'm quite familiar with this kind of crap..
Most important of all: treat the spots that rust *properly*. If you do a quick job (just cover them with paint) you'll find yourself treating the same spots over and over again - and they'll become much larger over time. If you don't remove rust completely it *will* come back.
First, you need to sand off the rust as much as possible.
For the small chips I found one of those glassfibre pentype things (Motip makes one I believe) the easiest to work with. Don't worry too much about hitting the surrounding paint (the *immediate* surrounding paint ofcourse ;)), this will help the new paint stick better and you can usually buff out these small scratches. Go sloooowly tough. You'll find that these small spots will take more time than the larger areas.
For the larger areas, get a dremel of some sort with various wire brushes and a few of these grinder stones to remove all rust. Also check for rust under the surrounding paint, as it can creep a long way hidden under the paint.
By now, If you've done things properly, you've probably removed quite a bit more paint (and metal) then you were hoping for, but remember that rust is like cancer, by cutting it out you're doing something good for the car.
Anyway, because you can never totally remove rust, you should shop for a rust-converter. There are various types, one is a combined primer/rust converter in a touch-up type jar, suitable for small spots, and the other one is just phosphorus (?) acid which you brush on, leave on for a couple of hours and rinse off with water - this is useful for the bigger areas.
What these products do is that they convert the rust to a "stable" oxide, the rust will turn black when converted and will stop spreading. A bit like how aluminium rusts, if you're familiar with that.
If the rust converter has done it's work, degrease, primer & and paint. Don't sand off the black spots left by the rust converter though.
I've found spraypaint more easy to work with even for touchups because it's thinner than the paint in those touch-up bottles - just spray some in the cap of the can and apply it with a small brush or a toothpick. Work slowly and in thin layers - try not to 'paint' it on, instead try to let a small drop 'flow' in the chip/scratch by capillary action. If your car is metallic (looks like it), you'll need to cover it with clearcoat too.
You're now probably left with 'bumps' instead of chips, flattening these is a kind of voodoo I'm still perfecting myself, but in general: wait for it to cure a little, wrap a rag around something like a creditcard, saturate the rag with an automotive paint cleaner (or thinner, if you're really couragous and need to clean up a big mess) and start polishing - don't apply much force, the idea is that you only want to hit the 'bump' and not the regular paint. With this technique I've managed to blend in some scratches perfectly, on others it didn't do anything, and on some I pulled out the touchup completely and had to start over again. Hit-and-miss kind of thing, but you might want to give it a go.
Your car doesn't seem to need it (but we'll see after you've sanded off all the rust :winkeye:), but for really large areas, go with spraypaint, mask off everything in the area. Try to paint one complete area that is 'naturally' delimited by trim or shutlines. If that's not possible (I don't think you can do much more than about 10 inches nicely as an amateur with a spraycan), never make sharp masks with tape: you will see the line *forever*. Instead, create a "crater" with tape and paper around the area and when spraying, try to minimize the time your spend around the edges of the "crater". However, never start or stop spraying on the exposed area, always start and stop on the masked area. If you need to cover with clearcoat, make a larger crater for the clearcoat and repeat - remember that it's not that hard to blend in clearcoat when polishing.
Furthermore, the usual applies, work in many thin layers, degrease etc, follow the instructions.
Also, use some filler and sand really really well because any imperfections in the surface are highlighted when you've got paint on.
After the clearcoat, the paint usually looks dull, but don't worry about this too much. Just let it cure for a few days and then use some cleaner, polish and elbow grease and it'll shine in no-time. Don't worry.
Some underbody coating before the paint on the edge of that wheelarch will prevent further stone chipping. While you're out there, remove the plastic splashguard and clean and closely inspect the area out there - dirt tends to clog the drainholes there and causes a lot of problems for both the outer panel and the floorpan.
The corner of the window is another typical E30-spot, and usually it means there's a lot more rust under the window trim...
Usually caused a combination of damage done when the window was replaced, and a slightly leaky window seal (next time you wash the car, keep an eye on that corner of the window and see if the water 'dissapears' )
That door seems to hang a little too low, might very well be the cause of that rust over there. Remember that by now it most likely rusts on the inside too, so you might want to get in there with rust converter and some protectant too. Unfortunately, from what I remember, that particular spot is almost inaccessible from the inside..
You might be able to tackle the dodgy touchup with the "creditcard" strategy above, but usually this touchup paint sticks very well where it shouldn't, and not where it should (see also: superglue

)
For the scuffmarks I'm still thinking of a strategy for my own car.. I think giving it a very light misting with spraypaint and a whole lot of buffing might do the trick.
Just some ramblings from my side, I'm in no way an expert, and I bet somebody here will come up with better advice, but still hope it helps..
Good luck,
Rick