In terms of plain mapsets, BJ Rowan's Conflict in the Fatherland comes to mind immediately, and the first Acktung! also easily qualifies. The later WolfBels (minus the creator maps of WolfBel3) seem good enough as well. I must sneak Temporary Insanity in there too, if you can find the right EXE to play it with. For Spear, I think of Spearmpixsod as well as Alliance of Powers.
For mods that are close to mapsets, Gary Ragland's works easily make the mark for me. Chemical Warfare also deserves a sure mention, and is sadly underappreciated IMO. I guess Revial of Memories should be mentioned as well, though it's from early 2006, but it follows from the WolfBel series of plain mapsets, being equal or superior in quality.
In terms of partial conversions, Totengraeber is obviously an instant candidate for me. BMSE orgiginal and The Golden Episodes also come to mind.
For total/near total conversion, Spear Resurrection and EoD obviously. WSJ's Dos mods as well, espeically Eisenritter and Coming of the Storm. And I'm going to include Operation: Letzterschutz too - as that was really good I felt.
How about you? It doesn't have to be in as much detail as I gave, just whatever comes to mind is good!