One possible way to do this is to create your own set of parameters. Say we call them DeployIisAppPath_One, DeployIisAppPath_Twoetc. Whatever names work for you, as long as they are unique.
Then do a little editing in each project file that you want to deploy. In the very first section, <PropertyGroup>add the following line. For instance. in the first project add
<DeployIisAppPath Condition="'$(DeployIisAppPath_One)' != ''">$(DeployIisAppPath_One)</DeployIisAppPath>
In the second draft, simalarly:
<DeployIisAppPath Condition="'$(DeployIisAppPath_Two)' != ''">$(DeployIisAppPath_Two)</DeployIisAppPath>
, . :
msbuild ... /p:DeployIisAppPath_One="MySite/one" /p:DeployIisAppPath_Two="MySite/two" ...