The newer release combined with the other two Eastwood movies, is there a big difference between the quality of the two High Plains Drifter movies? Or are they the same movie just repackaged?

The newer release in the 3-pack is anamorphic, while the old stand alone release is not.

I noticed on Amazon a new release of High Plains Drifter dated Feb 2009.
Is this just a re-release or a newly remastered DVD?

Dunno, but the version in this three-pack is 16x9, also costs $9.99 (5/20/2009 at Amazon,) and includes 16x9 versions of 'Joe Kidd' (John Sturges) and 'Two Mules for Sister Sara' (Siegel.)