Spybot-S&D is packed with useful tools and options than Windows Defender but the malware detection is very poor. Windows Defender may have detected more malware than Spybot-S&D, but it is not good enough for it failed to detect half of the malware samples. Knowing that their protection is to complement only the resident protection by your antivirus program, make sure that you are using advanced protection by an antivirus program e.g. AntiVir, Microsoft Security Essentials, Avast, VIPRE or NOD32 etc. If you need additional or on-demand malware scanner, consider using Malwarebytes Anti-malware Free, A-squared Free, Ad-Aware Free, or SUPERAntispyware Free.