spyware == an application that normally records the usage behaviour
and reports its findings back
like a browser helper object or like a layered service provider dll
and thier likes
they are a nuisence to have running not destructive or doesnt tend to perform illegal actions

while a trojan is a program that masquerades as a beningn (harmless )application but can be used for destructive purposes and illegal purposes
by the one who installs it in your system
for example a trojan can turn your system into a denial of service robot
which floods a site with numerous requests in order to deny the
regular user a chance to visit the site

so an application that basicallly targets trojans wont remove applications that are spywares and an application which targets spywares wont remove trojans
though there will always be some applications which are amphibious
that is they may be classified as a trojan and spyware also in the same breath