With this issue, you need to look at which programs you need. In my case, I still need to [unfortunately] run Windows on one of my rigs, because some of the CAD programs I use simply won't install under Wine.
Check out the appDB at the Wine website (linked earlier), and see if the programs you're wanting to use are supported. If they are, you're good to go. If not, start looking for open-source alternatives. There are plenty of free programs out there (like in my case, Blender, which I"m simply just too lazy to learn to use) that will work just as well or better than their Windows counterparts.
If you can't get the program to run through Wine, and can't find an alternative, then you're pretty much forced to either dual-boot or run a VM.
Good luck.