I have a bass tracker and it is getting stained really bad. How do you guys clean up your boats?

0000 steel wool and a bucket of soapy water. Pretty much just polishing the paint or clear coat. DO NOT DO THIS WITH FIBERGLASS BOATS OR MOTOR COWLS.

There's a few ways to do it and it depends on how you want it to look when it's done. There are several acid based cleaners out there to remove the oxidation as well as stains (sharkhide is popular). Many of these are marked for pontoon owners as many sit in the water all summer and look like crap when they get pulled out. Search pontoon cleaner or aluminum cleaner. These are easy to apply as you spray on and rinse off.

 Kevin's way will work as well if you wish to go that route. This could be a cheaper option as well.

 Once you get it clean you can take it a step further and polish aluminum to many different levels if you so desire. You can make it look like chrome even if you want to put that much effort in. Whatever you choose you should be able to find some aluminum sealer to help keep it clean in the future. 

star brite and a pressure washer