there are a crap ton all over
so it all depends on what you want to drink.
Green dragon (owned by rouge, mostly a tap house, but they have a brewery in the back), cascade barrel house (if you're here tuesday, go to tap it tuesday, always fun!) and hair of the dog and lucky lab is all within walking distance. (if you don't mind a 8-10 block walk, enough to sober up a titch
)
HUB, Gigantic, P.U.B. (portland u brew, tiny brewery with a homebrew shop attached) are all kinda close.
Just for the experience, you need to stop by either McMenamins, Kennedy school or Edgefield (in troutdale, just outside of portland east)
Although the "Big'uns" are fun to visit, Widmer, Dechutes, Rogue, Mactarnahans/Portland brewing, HUB.... all are fun..
But if you're only here 3 days... I'd say the NEED TO VISIT ones are
McMenamins Edgefield or Kennedy school.
Cascade if you like sours, walk over to hair of the dog and lucky lab
Widmer is in a fun little spot and you can walk over to another mcmenamins (White eagle)
HUB and gigantic are super close to each other
those are my votes... but i wouldn't hesitate to do a pub crawl!
http://beermapping.com/maps/citymaps.php?m=portlandor#lat=undefined&lng=undefined&z=2