For the game I made (54 Fantasy), XP comes from making a successful skill check (in or out of combat) with the caveat of it being "significant use" of the skill (for example, jogging through the dungeon won't give a point for using Athletics (Run), but trying to outrun the city guard probably would). Also, if you botched a check (the equivalent of rolling a 1), you gained experience for "learning from your failure". After gaining so much XP, you can spend it to increase skills.
Also, I liked Chronicles of Ramlar Experience Wheels - it was a circle with ten dots inside, sort of like a clock. In the center, you would write a goal - "Get Stronger", "Rule the Kingdom", "Become a Sky Knight", etc.) For every hour or significant action spent on activities that fulfilled your goal, you checked off a box. Once all 10 circles were filled, you completed the goal and would gain an advance in whatever goal you were working toward; this would be skill points, attribute increases, gaining prestige classes, ruling the kingdom, etc.