If Estonia goes to Germany:
Heinrich Himmler provisionally approved the General Plan East in June 1942. He further demanded a more specific "Overall Settlement Plan" and escalated the program to include "the total Germanization of Estonia and Latvia," along with Poland, "in no more than twenty years" and the "total resettlement" of Lithuania's population.”
(Blood and Soil, by Ben Kiernan)
“Jews were to be resettled wholesale; only certain proportions of other ethnic groups, spelled out in Wetzel's evaluation, were to be subject to resettlement. In the case of Lithuanians, Latvians and Estonians, this proportion was set at 50%....
The colonization enterprise was to be preceded by the takeover of the territories due for settlement, their economic exploitation for the duration of the war, and the expansion of the resources of the "German folk land" (deutscher Volksboden). With regard to the latter, the lecturer emphasized its great importance in view of the fact that it was meant to allow for the territorial concentration of the German people. According to notes taken by Hermann Krumey, Beyer listed Estonia, Latvia, the Dniester, Kiev and the Black Sea as border areas. For the time being the Protectorate of Bohemia and Moravia was not to be included in the projected settlement. Nonetheless, according to the variant of GPO developed by the RSHA, within 30 years 1-2 million German families were to be settled (45-50,000 per year over the first 10 years, and 20-30,000 per year for the following 20 years).”
(The Shoah and the War, by Asher Cohen, Yehoyakim Cochavi, Yoav Gelber)
In the early months of the war, all things seemed possible to the German conquerors, and Rosenberg and other Nazi planners anticipated the eastward expansion of Estonia's borders to the Leningrad-Novgorod line (a region that Rosenberg called "Peipusland"). Much of the ethnic Estonian population was to be moved into this area to make room for German colonists in the Baltic itself. In fact, such plans were seriously discussed at Hitler's headquarters as late as August 1942, but the Soviet counterattack prevented their realization. Along similar lines, the Generalplan Ost of the SS Planning Office in May 1942 called for the population of the eastern Marken (frontier regions) to be substantially German or Germanized within 25 years.”
(Estonia and the Estonians, by Toivo U. Raun)
“The Plan to Germanize the Ostland During the German occupation Estonia (which was extended at the expense of Great Russia to include Novgorod), Latvia (which was extended to Velikie Luki), Lithuania, and Belorussia or White Russia (which was extended to include the Smolensk region) — all these areas were joined together in the Reichcommissariat Ostland.”
(Augustana Library Publications)
Himmler said: "We must Germanize and colonize White Russia, Estonia, Latvia, Lithuania, Karelia and the Crimea. We will proceed in other areas as we have begun here, building small cities of 15,000 to 20,000 inhabitants, along lines of communication where our super-highways, railways and airports are protected by our garrisons, and surrounded by a ten-kilometer radius of villages, so that the people are always immersed in German life and related to an urban cultural center."
(History vs. Apologetics: The Holocaust, the Third Reich, and the Catholic Church, by David Cymet)
“As possible destinations for the Jewish expellees, Rosenberg suggested the territory eastwards of Lake Peipus on the Estonian–Russian border and declared that 'a great possibility for settlement' existed, above all, in Belarus"
(Exploitation, Resettlement, Mass Murder: Political and Economic Planning for German Occupation Policy in the Soviet Union, 1940-1941, by Alex J. Kay)
Summary: Nothing particularly enjoyable for the Estonians.
If Hitler didn't decide to be a complete asshole when it came to Estonia:
“The Nazis capitalized on the Estonian quest for the Finno-Ugric ideal rather than pushing them in that direction. Estonian president Konstantin Päts, shortly before his arrest by the Soviets... suggested the relocation of the Estonian and Finnish borders eastward so that they could include the Finno-Ugric minorities. Päts also proposed replacing Estonia's Russian population with racially similar peoples from Russia proper. According to Päts, the Finns should have carried out a similar resettlement program in Karelia. The 1939 Soviet aggression against Finland made many Estonians feel guilty for not having helped a brother nation in need. The Estonians could now claim to repair that moral failure by assuming the symbolic role of caretaker of the Finno-Ugric nations in the German-occupied territory of the Soviet Union. Considering the close ties between Finland and Estonia—even if the former had usually played the role of leader and the latter of follower—the Estonians were now psychologically relieved of a possible inferiority complex. In practical terms, however, the Estonians could do little to help their linguistic kin in Ingermanland. The only thing Estonians could eflectively do was to extend to the Finno-Ugric peoples of Russia the notion of a common culture and spirit. Before the war this attempt was realized mainly through ethnological studies, while in the context of Nazi occupation it came to be conveyed through anthropological and racial studies.”
“The Nazi “New Europe” was to be created through population transfer. The resettlement of Baltic Germans in the fall of 1939 (so-called Urnsiedldng) marked the first phase of the ethnic restructuring of the continent. In the northeastern corner of Europe, Estonia and Finland became actively involved in executing the racial blueprints of the Nazis. This involvement distinguished Estonia from the rest of occupied Eastern Europe, which had, for the most part, remained a passive recipient of the population policies emanating from Berlin. What Estonian and Finnish ethnologists and linguists had until now only dreamed of—a greater Finno-Ugrian entity—was becoming reality. Although it did not result in any significant increase of political representation, the demographic remodeling of the areas located between the Baltic Seain the west and Lakes Ilmen and Ladoga in the east echoed the interwar rhetoric regarding a pan-Finno-Ugrian union of sorts. Once again, the Nazis attempted to build a bridge to the hearts and minds of Estonians. The repatriation of ethnic Estonians from former Soviet territories had long been on the agenda of Estonian politicians and intellectuals. The German Security Police supported this endeavor as long as it concerned racially fit Estonians. According to Head of the German Security Police in Estonia Sandberger, incorporating small ethnic groups from Ingermanland into the Estonian majority would advance the concept of the Nazi “New Europe.” When asking whether there was “more of a valuable Estonian and Finnish ethnic stock left in the Soviet Union,” Sandberger argued that the Estonians would cherish the idea that they had saved even a tiny bit of precious human material. Indeed, by winning it back to the Estonian nation they would have prevented the imminent decline of kindred peoples. Head of the Estonian Self-Government Mae went one step further, proposing to exchange Estonia's Russian population for ethnic Estonians and other Finno-Ugrians living in Russia.”
“Between 17 August and 15 September 1942 a group of TU professors and graduate students conducted a population study near the town of Kotly in Ingermanland. Among the most noted participants in the research expedition were the ethnologist Gustav Rank and the linguist Paul Ariste. Another member of the expedition was an Estonian agronomist in the service of the Security Police in Tallinn. The main objective of the study was to map villages with a predominantly Finno-Ugrian population. The Wehrmacht, which sponsored the research, was particularly interested in reviving Finno-Ugrian settlements in that area.”
“Estonians did not waste time speculating about “Greater Estonia," which their status as an occupied country could not afford them anyway. Instead, Estonians capitalized on the territorial gains that Nazi propaganda had promised them. Even then, Estonians approached the matter seriously by conducting scientific research on Finno-Ugric peoples living in the former Soviet territories.”
(Racial Science in Hitler's New Europe, 1938-1945, by Rory Yeomans, Anton Weiss-Wendt)
Also, Finland had some designs on Estonia.
(compiling all this stuff goes to Ulrich Norman Owen, the Nazi Victory Map dude)