I use CorelDraw, but only because I was taught how to use it by colleagues. It might be good to ask colleaugues what they use so they can help you learn how to use the program there. For 3D images, some people use Povray, it produces beautiful images if you can use it, but I can't.

I also use ChemBIoDraw. But my colleague use CorelDraw.

I agree with above comments, If you can use povray you can get nice 3D images some programming is required here.

Inkscape is a free and pretty nice alternative to Illustrator or Corel Draw.

If you need just vector graphics and text you could use Inkscape, if you need to visualize some data you could use gnuplot. Gnuplot also can perform some calculations, it has some built-in math functions (sin, cos, ...), can plot both 2d and 3d.

Inkscape is free or I suggest CorelDraw, for plots Origin

I use this little Mac program called LineForm for vector drawing, and it is pretty good. For molecules I use QuteMol, and it gives impressive high quality results. And you can also use VMD to generate Povray files. For data plots, qtiplot is a sort of clone of Origin, it works fine and it's a lot cheaper than Origin.

I agree with the suggestions made above. It is, however, nicer to provide information on free software, such that my favorite is actually the above mentioned Inkscape that even comes as portable version on Windows. Gnuplot is nice, but directly using python is probably better (mathplotlib, etc). Your question is for pictures for publication in journals. Many Journals still ask for *.eps format, so whatever software you use, make sure that it properly exports in the formats desired by the according journal. Concerning standard graphs, e.g., I usually export without axes labels, etc. In an intermediate step I use LaTeX and the pstricks package to add labels arrows etc. Note that LaTeX directly provides many plotting packages for 2D and 3D data and objects (pstricks, pst-3d, pst-2dplot, pst-3dplot, etc). The drawing in LaTeX is actually more programming, but the output is directly publication quality. And it is free and platform independent.

According to the last answer, *.eps format is still teh choice for submission? I have the experience that files can become very large, so there was no other choice to leave the vector option and convert them into *.png or others. That happened ven just with Excel plots. What would be the best advice?

Well Wilfried Wunderlich, the choice of *.png over *.eps is difficult, as they have different purposes of course. EPS is a container, but can contain vector information, while PNG is raster graphics. Hence, vector graphics has virtually infinite resolution compared to your once fixed raster. EPS becomes unbelievable large when putting e.g. STM images but for simple line plots it is reasonably small, unless you plot a spectrum with 150000 points. Then you have to save the full data in your EPS, while PNG just takes the coarse grain version. In this case, hence, it is a good idea to think about data reduction first.

The typical journals I submit to, still ask for/or at least except EPS format (see below). When writing a thesis or similar, I would use pdf-LaTeX and make my images as PDF, which can contain vector information and is usually significantly smaller than EPS.

From the "Review of Scientific Instruments" Author's page:

Scalable vector formats (i.e. EPS and PS) are greatly preferred. AIP Publishing suggests the use of Adobe Illustrator (Paid, OS X, Windows) or Inkscape (Freeware, OS X, Windows, Linux) for the creation of acceptable illustrations and Adobe Photoshop (Paid, OS X, Windows) or GIMP (Freeware, OS X, Windows, Linux) for the editing of acceptable photographs.

If you're a Unix/Linux user, XFig is the simplest and, in my opinion, best tool for producing vector graphics. For advanced users, there are tutorials available that explains how to include LaTeX-coded text and equations into the images.

free and powerfull GNU-R

Inkscape for 2D and Blender for 3D pictures.

Blender for animations

For instance: https://www.youtube.com/watch?v=RasemoYzsFA

Inkscape for 2D and Blender for 3D pictures.

Blender for animations

For instance: https://www.youtube.com/watch?v=RasemoYzsFA

Mr. Harnois has provided a very good info for your need.

inkscape as well as blender are great, free and light weight alternatives  and available for both windows and linux.

Inscape is the best for the purpose (it creates pictures with vector graphics approach by default)