Vologda was firstmentioned under year 1147. It was major transit city before St.Petersburg was founded (1703). 1565-1571 Ivan the Terrible proposed Vologda as 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 forward and 14:25 return. Price is reasonable and competitive with train. Airport is situated 8 km north from city centre, easily reachable by bus or taxi.
Nearest international airport is Cherepovets (CEE) (see http://wikitravel.org/en/Cherepovets for details)
Train is still most convenient approach to get to Vologda. Vologda stands on intersection of railways Moscow-Arkhangelsk and St.Petersburg-Ekaterinburg. You can get from St.Peterburg Ladozhsky station for 12 hours, 3 trains both day and night or from Moscow Yaroslavsky station for 8-9 hours, 6 trains a day (see pass.rzd.ru for details).
Vologda is 470 km to the north by the M8 road from Moscow. It takes 5-7 hours drive 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 GPS navigator is recommended.
There are some direct bus lines from 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 ticket (16 RUB) at the conductor or driver. You can save on several routes with 15- or 30-ride smart-cards (15 or 14 RUB for ride respectively). Smart-cards are valid on all trolleybuses and buses with red-square "Zabota" sign.
Atrium Hotel, ul. Gertsena, 27, ☎ +7(8172) 78-78-25 (firstname.lastname@example.org, fax: +7 (8172) 75-33-13), . This business-class hotel is centrally located, easily found while driving, and newly built. Rooms are comfortable, 4 stars are claimed, at least 3 stars are really delivered. Free wi-fi in rooms and lobby.single 3,400 - 4,600 RUR, double 3,800 - 5,000 RUR dependig on room class. edit
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