One of the genuine pleasures of visiting Japan is the quality of food available in ordinary supermarkets and convenience stores, and Tsukuba is an excellent place to experience this. The city's large research population — many of them working long hours and eating alone — has created sustained demand for good ready-made food, and the selection reflects it.
The supermarkets around Tsukuba Station and in the Creo shopping complex stock fresh bento boxes at lunchtime and in the early evening: rice with teriyaki chicken, katsu curry, salmon with pickles, mixed sushi sets. Quality is consistently higher than you would find in equivalent convenience food in most other countries. The onigiri (rice balls) at any Family Mart or 7-Eleven near the station are a fine breakfast or quick snack before catching the Tsukuba Express back to Tokyo.
If you are spending a full day in Tsukuba and want to eat cheaply and well — particularly if you are hiking Mount Tsukuba and want to pack a lunch — the supermarket bento is the obvious choice. The mountain base has no food service once you are on the trail, so buying provisions at the station before departure is sensible.