DE2 GPIO pins are basically LVTTL (3.3V logic) digital IOs. Data direction (input,output, bidirectional) has to set up for each pin in the FPGA project. The GPIO pins also have clamp diodes to 3.3V supply. Using external series resistors, you can drive them from 5V logic. 5V supplied TTL compatible logic (e.g. HCT74 family) can also be driven from 3.3V GPIOs.
The board has no analog inputs apart from audio and video codecs. To capture general analog inputs, you should connect an ADC chip. For slow signals, an ADC with serial SPI or I2C interface seems to be the most suitable method.