I'm posting here five maps for all the ancient mtDNA I know of. Mostly compiled from the Ancient Eurasian DNA site, but checking the references when I thought necessary. Two of the maps have been posted here before.
Paleolithic and Epipaleolithic:
Already commented here.
Updated (Oct 8): a likely H individual from Villabruna (Trentino-South Tirol, Italy) from Di Benedetto 2000 belongs also to this period (c. 14,000 BP) and is also an important counterpoint to the apparent U dominance of Central Europe, somehow ratifying my idea of H being common throught the south of the continent already in this period.
Neolithic and early Chalcolithic (up to c. 3000 BCE):
Already commented here.
Late Chalcolithic and Bronze (c. 2800-1000 BCE):
Note on Germany: the Eulau (Saxony-Anhalt) and Liechtenstein (Lower Saxony) sites are not too distant geographically but, in time, they are at the extremes of the temporal scope of this map, with Eulau belonging to Corded Ware (c. 2600 BCE) and Liechtenstein Cave to Urnfield culture (c. 1000 BCE). This may be an important reason behind the quite radical differences in the mtDNA pools, though I fail to understand well the processes that might have been involved; after all both were Indoeuropean cultures, right?
Nevertheless, while Corded Ware would seem to express influences from the East (Poland and beyond), Urnfields belongs rather to the West, being its core area at the Rhine. Why would this make a difference? I am not sure but I have read that in the late Bell Beaker there may have been a real demic replacement in the Rhine area (from the Austrian-Czech area?). This might have allowed for founder effects that later spread with Urnfield culture maybe. Just a tentative conjecture anyhow.
Another possibility could be the older influence of Megalithism and "collective burial" (clannic burial probably) cultural package directly in that region (but not in East Germany).
Note on Basques: the three Basque samples of Izagirre & De la Rúa for this period are shown as two: I have merged the two samples of Biscay but shown as distinct the one from Navarre (Longar).
Antique and early Medieval (c. 600 BCE-800 CE):
Note: map updated (Oct 6th) in order to include the Iron Age Iberian data of Sampietro 2005.
Notice how Britain and Denmark already show a high apportions of H, as is the case of Italy (and SE Romania too in the previous map). While this says nothing directly on the previous situation, it may suggest that either (1) H was relatively high in southern Europe (besides Iberia) already in Paleolithic times and that (2) H spread (partly?) with Megalithism through the Atlantic. Still conjectural anyhow.
Take note also that one of the Italian samples is attributed to Luke the Evangelist (hence presumably of Syrian origin, haplogroup H2a2).
Late Medieval (c. 890-1300 CE):
Most noticeable is maybe the still relevant presence of N1a (2/27) in Medieval Hungary, haplogroup also found in the Danubian Neolithic that originated there. This really suggests that, in spite of its apparent numerical decline towards the present, European N1a can be rather safely considered of Middle Danubian origin. Haplogroup I, while not a direct descendant, is a close cousin of N1a and may have also coalesced in Central Europe.
The small Italian sample in this map belongs to Francesco Petrarca (J) and a woman buried in the same tomb (H).