I have NEVER had spam or dubious popups on my PPRuNe account when used via the web.
BEags et al:
Investigate Google toolbar - it has a pop-up ad killer. Also check
http://www.meaya.com for their Pop-Ad Filter, and
http://www.geocities.jp/baryonlee/noflash/ for NoFlash - which stops all sorts of unwanted bandwidth hogging stuff.
AND use Ad-Aware or SpyBot to ensure you've got nothing lurking on your machine which you don't know about.