The voting process is easy - simply go to the ModDB/IndieDB profile of the project you want to vote for, click on Vote Now, and you're done! You have until 11 December to do so, at which time the Top 100 mods and Top 100 indies will be unveiled, which will have their own voting process afterwards. On the 22nd, the Editors' Choice will be published, followed by the Players' Choice for unreleased projects on the 27th, and on the 29th, we'll know the Players' Choice for released projects.
Also, voters are eligible to win some games! So get voting, help your favourite mods and indies get to the top, and you might just go home with an extra game! You can find further information here for ModDB and here for IndieDB.