Vologda was first mentioned in the year 1147. It was a major transit city before St.Petersburg was founded (1703). From 1565 to 1571, Ivan the Terrible proposed Vologda to be the new capital of his domain (instead of Moscow).
VGD airport provides regular flights from St.Petersburg only (since Aug 12, 2013), three flights a week - Mo, We, Fri (pskovavia.ru, agent.ru) 10:10am there and 14:25 return. The price is reasonable and competitive by train. The airport is situated 8 km north of the city centre, easily reachable by bus or taxi.
The nearest international airport is Cherepovets (CEE) (see http://wikitravel.org/en/Cherepovets for details)
The train is still the most convenient way to get to Vologda. Vologda stands on the intersection of railways Moscow-Arkhangelsk and St.Petersburg-Ekaterinburg. You can get there from St.Peterburg Ladozhsky station in 12 hours, 3 trains (both day and night) or from Moscow Yaroslavsky station in 8-9 hours, 6 trains a day (see pass.rzd.ru for details).
Vologda is 470km north of Moscow by the M8 road. It takes 5-7 hours of driving to reach the city, depending on traffic. Road conditions are generally good for Russia, excluding the total mess with street navigation when passing Yaroslavl. So, using a GPS navigator is recommended.
There are some direct bus lines from the Moscow airports to Vologda. They are rather cheap, but it is difficult for international passengers to use this option (see, for example, http://kucher35.ru/service.php).
Public transportation in Vologda is rather good. There are buses and trolleybuses. You can buy a ticket (16 RUB) from the conductor or driver. You can save on several routes with 15- or 30-ride smart-cards (15 or 14 RUB per ride respectively). Smart-cards are valid on all trolleybuses and buses with red-square "Zabota" signs.
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Semenkovo Wood architecture museum - bus 37 in "Molochnoe" direction, 30 minutes from city center
Spaso-prilutsky monastery bus 28 (to Priluki), bus 22 (to Semenkovo - don't confuse with Semenkovo museum!), bus 36 (to Aviator/Aeroport) 20 minutes from city center
Kirillo-Belozersky monastery regional buses to Kirillov from bus station near railway station, 3 hours to go
Ferapontov monastery regional buses to Lipin Bor (note - Ferapontovo is not a terminus), 3,5 hours to go