Is there a way to show junctions differently in windows explorer?

You can use the Link Shell Extension. That will use a different icon for junctions and links.

Be warned, that deleting a junction from Windows Explorer will in fact delete the target folder, therefore I would recommend using some other file manager like Total Commander - it shows junctions with a different icon.

Update: As of Windows 7, deleting the junction won't delete the target folder anymore, so this has apparently been fixed.

I've used NTFSLink and found it effective: http://elsdoerfer.name/ntfslink

It also makes the behavior a bit more intuitive particularly vis-a-vis deletions.