One week late... this is my perspective on what happened in Estonia. In terms of facts, I don't have much to add to what Aleks and Justin wrote.
Why did this happen in Estonia and not Latvia? There are a few curious stories that I've read over the past months. The first was in Nedela (The Week), a Latvian newsmagazine, last December. A certain pro-Russia activist organization was planning to organize a "conference" in Riga on World War II and Latvian history. Given the organizers, the conference would have been a sequence of speeches proclaiming the positive role of Soviet Union, denying that Latvia was ever forced to join the Soviet Union, downplaying the extend of Stalinist crimes against humanity... They got a phone call from Russian embassy in Latvia asking them to cancel the conference.
The next story came in March. March 16 is a date when the Latvian legion of SS was founded in 1943 and it usually results in a number of marches and counter marches in Riga, by older veterans who were part of Latvian legion, by younger Latvian nationalists (a lot of them from quite dubious nationalist organizations) who want to honour the Latvian legion and by Russian groups who hate the legion and try to obstruct the march, proclaiming that "freedom of speech does not apply to Nazis". In past years, things have gotten quite confrontational, to the degree that Riga City Council deliberately scheduled repair work in the city centre in March 2006, to push the marchers away to more remote locations.
This year, there was a new twist! A few phone calls from Russian embassy to "anti-Nazi" groups asking not to get "too unruly" with their "counter-march" because Russia did not want to inflame tensions in Latvia. The organizers were hinted that, if they disobey the orders, they might run into some dificulty getting Russian vizas next time when they go to Russia.
If Moscow wanted to stir up tensions in Latvia, they could easily find an excuse... but they seem to be working in the opposite direction! Why are they interested in confrontation in Estonia but not Latvia? I wish I could understand the logic of Moscow puppetmasters...