On color
Generally, use dark background in a dark room; light background in a well-lit room or room with plenty of natural light. Once you’ve picked dark background, then use light color for fonts and graphical components; vice versa for light background.
I found it useful to actually project a color wheel onto the screen and check if there is any segment that is not distinguishable. I personally found yellow-red-brown spectrum usually fails, and I tried to avoid using them to show gradient data.
If a graph can do the job with just black and white, then keep it black and white. Blue themes are deemed the most color-blind-friendly, while red-green combination is a usual culprit to avoid. Brewer has made a website for choosing map colors. There you can also pick themes that are colorblind safe and, more importantly, photocopy-able. Color charts are doomed if they lose information after photocopying.
Line/shape and font
Whenever I have a chance, I’ll go to the room that I’ll be presenting and use the beamer there to project some reference slides (see the attached image). You can make one for fonts, one for lines with different thickness, etc. My general impression is that sans serif works better when the on-screen resolution is low.
Format
I use .png for simpler graph and illustration and .tif for maps. I have not encountered any problem so far. I like that these two formats can tolerate a good degree of manual enlargement. In case if the audience really wants to see the picture up close, I can still do that without it turning pixelated.
Print
For very complicated graphs, I also brought print outs. A trend that I have been seeing in lectures is that more and more attendees are loading up my presentation on their computer while listening to me. The benefits are that they can see the graphs up close, and they can also take notes directly on their computer. So, I would also recommend at the beginning and the end, provide a link to the crowd in case if they'd like to download your work.
References
Since the question isn't about how to make good graphs, I'll save all those Clevenland and Tufte materials. Although, I have to say that Tufte's principles on data-ink ratio have been very helpful, as long as you know when to stop following his advices.
For online presentation, I'd recommend books and website by Garr Reynolds. His book Presentation Zen is pretty useful.
