Rage seems to have posted a rather intuitive reply, but maybe these will offer other solutons as well. 
-1 It doesn't matter what I select in the Rendering Globals window for camera to use during batch rendering, it always renders my perspective view first, and only after that it renders my selected camera, wich is definetely very annyoing since I have scenes of +- 900 frames. Is there any way I could make Maya render only my selected camera?
You have to SET THE PROJECT to get the cameras to work properly. If you don't, then you will have rendering issues. Also, in the attributes for the perspective camera, in the Render Attributes turn off RENDERABLE.
2- Maya autmotically sets, if I use 'clouds' for particles, the clouds to particleShape1. Wich means I can't use more than one colour particle clouds.
Create a new Particleshape Node.
3- OpticalFX, or lights in general; can they be set with the time slider to increase/decrease over time, or how can I make my OFX appear only a certain number of frames?
You can animate any attribute for any item by setting keys for it. Simply select the start point in the time line to place your first key. Then in the Channel Box, click on the NAME of the attribute you want to set keys for, RIGHT CLICK on it and choose SET KEY. Go to the next place in the timeline, adjust the attribute value and set a key again. For instance, if you want to turn a light on and off then you would set keys for the INTENSITY of the light. 0 is off, 1 is on.
4- Painting. What is the best way to display, let's say galactic brush paint strokes?
You need to set up a paintable geometry. For the galactic brush, you'll want a flat plane set sideways on the x or z axis. Make it paintable, then paint it.
5- What file extension must I use to render my scenes quickest? And does anyone know what resolution an overhead projector uses?
Maya IFF seems to be the fastest file extension for me. However, you won't be able to open it in photoshop. You can, however, convert the files in FCHECK to JPEG. I'm not at my PC at this time so I can't elaborate on how to do that just yet. I'll come back later and edit this when Im back on my unit.
As for the overhead projector, whcat kind of overhead projector are we talking about? Slide, transparency, or digital display?
6- Using a 'real' vortex, is there any way to create a vortex that draws particles to it? I've already tried to make create a vortex with some other field that have a stronger attenuation/
magnitude but that is quite... instable.
There are many different tornado tutorials out there on the next. Do a google search for them and find one. But what you're trying to achieve requires the addition of collideable geometry. You need to make a 'funnel' that the particles will form to when they emit. You'll also need to apply a gravity field to the particles in order to draw them upward.
Hope that helps.
Dave Baer
Professor of Digital Arts
Digital Media Arts College
Boca Raton, Florida
dbaer@dmac.edu