Fonts will look different regardless of the changes you make, since Eclipse is based on SWT and NetBeans on Swing; two sets of user interface tools use different font rendering mechanisms.
Some fonts look better than others in Swing. My preference for Swing (and almost everywhere I use single-spaced fonts) is Ubuntu Mono , but Deja Vu Sans Mono and Pro Source code are well displayed in Swing too.
You almost certainly have the first two on your system, and the third is simple enough to install if you want. I will say that the Pro line source line pitch is great for my taste, although otherwise it's a good font.
After turning on the JRE flags that you mentioned and choosing the appropriate font, the next important element is to choose the best font size. This font in this rendering engine may look better or worse at a given size than in another environment.
I find that in Swing Deja Vu Sans Mono looks better even in dot sizes, so I usually use it both 10pt and 12pt in NetBeans. Ubuntu Mono, on the other hand, does a lot nicer with odd sizes, so I usually use it in 11pt or 13pt in NetBeans.
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