There is no reason why you couldn't do this; you could just copy it into your DNN portal (assuming it is an ASMX or SVC file?) and if it is precompiled, copy the DLL into your BIN folder.

As an aside, putting a webservice into a module is also not out of the question either.  I frequently build webservices with my internal modules (at my day job) which I expose functionality to all sorts of other applications including other web apps, windows apps, windows services, etc.  Since they are packaged up with a module, however, the URL to access them is a little bit different (http://yourdomain/DesktopModules/yourmodule/yourfile.asmx).

Go for it though, webservices make things handy.

*EDIT*: BTW, for anybody using WebServices in a DNN module in general there are some caveats.  For one, the HttpContext within the webservice doesn't seem to populate portal details so you have to trick it.  I use the following method that I wrote to "initialize" a portal call (note that the idea for the "MacuAuthentication" object comes from Michael Washington's "secure webservice" tutorials):

// utility members; used for loading info for modules
private DotNetNuke.Entities.Portals.PortalAliasController _pac = null;
private ArrayList _portalAliases = null;
private DotNetNuke.Entities.Portals.PortalSettings _ps = null;
private DotNetNuke.Entities.Tabs.TabController _tc = null;
private DotNetNuke.Entities.Tabs.TabInfo _ti = null;
private DotNetNuke.Entities.Modules.ModuleController _mc = null;
private DotNetNuke.Entities.Modules.ModuleInfo _mi = null;

internal void InitializeCall(Macu.DNN.Web.Services.MacuAuthentication auth)
{
_pac = new DotNetNuke.Entities.Portals.PortalAliasController();
_portalAliases = _pac.GetPortalAliasArrayByPortalID(auth.PortalId);
_ps = new DotNetNuke.Entities.Portals.PortalSettings(auth.TabId, _portalAliases[0] as DotNetNuke.Entities.Portals.PortalAliasInfo);
_tc = new DotNetNuke.Entities.Tabs.TabController();
_ti = _tc.GetTab(auth.TabId, auth.PortalId, true);
_mc = new DotNetNuke.Entities.Modules.ModuleController();
_mi = _mc.GetModule(auth.ModuleId, auth.TabId, true);

// set contextual info
HttpContext.Current.Items["UserInfo"] = auth.UserInfo;
HttpContext.Current.Items["PortalSettings"] = _ps;
}