Tsukuba's position on the Kanto Plain puts several interesting destinations within reach for a day trip, either from Tsukuba itself or combined with the city on a trip from Tokyo.
Tokyo (45 min by Tsukuba Express to Akihabara) is the obvious companion: most people visit Tsukuba as a day trip from the capital, but it works in reverse too, with the last TX trains back to Tsukuba running until midnight. Akihabara, where the express terminates, is Tokyo's electronics and anime district — a useful contrast to Tsukuba's science research character.
Mito (1 hour by train) is the capital of Ibaraki Prefecture and home to Kairakuen, one of Japan's three celebrated landscape gardens. The garden is famous for its plum blossoms in February and early March, which predates the cherry blossom season and draws significant crowds. Outside blossom season it is a quieter, pleasantly old-fashioned provincial city.
Nikko (2 hours via Utsunomiya) is one of Japan's most ornate shrine complexes, built in the early seventeenth century as a mausoleum for Tokugawa Ieyasu, the founder of the Edo shogunate. The mountain setting, the elaborate carvings, and the long cedar avenue approaching the main gate make it one of the most impressive religious sites in Japan. The journey requires a change at Utsunomiya, but the routing is straightforward.