It looks as more and more people are getting caught out with downloading free programs and getting nasty extras in the bargain. I'm no expert but my advice would be check the site you wish to download from first. In my experience C|Net is a no-go for me. It has changed a lot lately. Softonic and File Hippo amongst the safest.
Whenever you download select the 'save' option, not 'run'. You have then the option to right click the file and scan with your AV and antimalware programs.
Once you're happy to install always select the 'custom' install option. This is very important as it allows you to untick and decline extras.
During the installation always read what is offered. If you have a series of boxes to untick, then always untick from the bottom of the list to the top. This is because if you tick a box at the top a lower ticked box might be greyed out so watch out for that one. You then might get a page with another product on it but with two buttons, one with 'accept' and the other with 'decline'. If its junk don't be afraid of hitting the 'decline' button. If this stops the installation then find another site to download from. If it continues to install, with no other options, then good.
I hope others can contribute some more tips on how to download and install as safely as you can and this is just for information for some of the unwary.
If you've just done a fresh install or reinstall and you need to download e.g. Chrome, Adobe Reader, iTunes. Avast, IrfanView and so on, I highly recommend ninite.com. Not only does it automate download and installation, but it's also malware free and cleverly answers 'no' to tall the questions you'd have answered 'no' to (like "Would you like to install the Jeeves toolbar?" They have a lot of stuff there although, of course, there's a lot they don't have. Might be a good place to start,though.