You wouldn't need to move your WSS sites  to the new server  unless that
is what you want to do. SharePoint Portal Server's site  Directory Area
can categorize the existing WSS sites right where they currently exist.

As for the tools, I don't currently have a strong opinion about what
tools are better for moving sites from one server to another. FWPs,
STPs, smigrate, stsadmin, backup/restore are all options. However, I
would need some time to create the grid of pros and cons. Does someone
with an opinion based on some experience have any thoughts on which is
better and why?

I know that STPs are only for a single site at a time and don't preserve
things list security. But that is what I tend to use most.

We are moving from WSS on a single machine  to a mid-sized farm. So
far, I've tried SMigrate. It has worked well, but there are a few
caveats. As Todd mentioned, the user rights do not migrate. This is
not a big problem if you use rights inheiratance. It is a big
problem if you have rights on different Document Libraries.

Also, you have to create the site  prior to importing it. Make note
to not apply a site template. The import will not work if you do.

I do like the fact that it is only one site at a time. We can
communicate to a smaller subset of users so they can stay out while
we move data.

had you considered using stsadmin.exe? Why not just re-connect Portal Server to your WSS content database? Is that an option?

In this case, I don't want any ties between the WSS server  and the
SPS server farm, not even for seaching. We are retiring the WSS
server. WSS was installed two years ago on old hardware then just to
see what SharePoint could do for us (see my sig below). We are
slowly rolling out SPS and cannot do a mass migration.

I'll try the other options. I've scripted
stsadmin to do daily backups, so it seems like the next logical test.

So, we decide to install Portal on a new machine. If we wish to connect to the WSS SQL content database to our new Portal Server Install, is that something that is done during the installation or is it done afterwards?

I think that stsadmin moves entire Site Collections (including security)
but I haven't done it myself.

After installation you can link to the existing WSS Sites and your SPS
portal can index and crawl the content as if it were embedded in the
portal's database.

This is what i was hoping. But once i create the Portal Site, i will have to manually add the URLS to each of the WSS sites, correct?

Right, but it isn't difficult. You will just navigate to the Sites
option in the top nav (that's the Site Directory Area) and click "Add
Link to Site" in the Actions section of the left nav.

Is there an advantage to embed the WSS sites  into the portal  database rather than keeping them in the STS database and connecting portal to them?

I don't think so but others say:
-It is easier to create new top level sites  thru the SPS site  Directory
Area (everything is auto wired up and indexed).
-Only SPS databases to backup and restore instead of SPS and WSS
databases.
-Only one IIS Web site

I'm sure there are other reasons given.