Actually, the latest weather report has a bit of clearing forecasted for Saturday and Sunday, so you may be in luck! But it is rainy season, so make sure you have an umbrella handy.
If the weather's clear, I'd suggest Insadong (though highly touristed), Gwanghwamun Plaza, and Gyeongbok Palace. They are all within walking distance of each other... You could take the metro line #3 (orange) to Anguk Station (안국역) exit #6, walk along Insadong (stop at Jogyesa Temple, a side-street over), and then walk down to Jongno. You can also see Tapgol Park (to your left) or Bosingak (to your right). You'd want to head towards Bosingak to get to Gwanghwamun Plaza, though. At Gwanghwamun Plaza, you can see the statues of Yi Sun Shin and King Sejong the Great. There is an intersresting (and free!) museum about hangeul, the life of Sejong, and Admiral Yi Sun Shin that can be entered at the rear of the Sejong statue. If you keep walking along the plaza towards Gwanghwamun Gate, you can enter Gyeongbok Palace. Admittance is just 3,000KRW and includes admission to the National Folk Museum and the National Palace Museum.
If it's raining, you could go to the National Museum of Korea... it's wonderful! You would just need to take the metro to Icheon Station (이천역), and the exit is clearly marked. Admission is free, excluding any special exhibits.
For information on the subway, check out this site.