In practice, it’s safest to download software directly from the original source, but not all companies are equally trustworthy. Microsoft and Mozilla (Firefox) should be fine, for example, but Oracle (Java) and Adobe will foist unwanted programs on you if you are not careful.
Many small software houses are trustworthy, but some have download links that take you to another site, such as Download.com. I know you won’t go there again.
If you are not sure which program to download, try Major Geeks or Gizmo’s Freeware, aka Tech Support Alert. Both have the same drawback: they concentrate on the top utilities, which means they’re missing millions of programs. Gizmo’s has better reviews of fewer programs, but it’s a community effort and not all its sections are up to date. I also use AlternativeTo, where programs are rated by people’s votes (likes or “social software recommendations”).
All three sites provide direct links to the official websites for program downloads. This is important because it means you can avoid using Google, and the risk of clicking any Google ads. As you have found, Google is not a good guide to download sites, and some ads may be even worse. (Google has distributed Chrome, Google Toolbar etc as crapware with other downloads, including Avast and Adobe Flash.)
But be careful: even direct download pages can trick you into installing things you don’t want. For example bagas 31, they may display huge green DOWNLOAD buttons that link to crapware, while the link you want is just one word of small, underlined text. Hover your mouse over the links to see where they actually go.
App stores and more
One solution would be a software repository that worked like the various app stores provided by Amazon, Apple, Google and Microsoft for smartphones and tablets. This isn’t foolproof because developers can still upload crapware, but at least the app store providers are trying to keep it out. Also, app stores work better for smartphone and tablet apps – which are small and very constrained as to what they can do – than for complex and powerful desktop/laptop software. Nonetheless, I expect the trend towards stores offering desktop software will continue.