Multiple left joins or subquery?
This is my best shot without seeing any table structures

SELECT
    user_runs.userID,
    user_runs.runID,
    `createdBy`,
    `username`,
    DATE_FORMAT(`dateCreated`,'%d-%m-%Y') `dateCreated`, 
    COUNT(DISTINCT runFavouriteID) AS favourite,
    DATE_FORMAT(MAX(`runDate`),'%d-%m-%Y') AS `lastRan`,
    MIN(`runTime`) AS `fastestTime`
FROM
    (SELECT * FROM `user_runs` WHERE userID=4) user_runs
    INNER JOIN `runs` ON user_runs.runID = runs.runID
    INNER JOIN `users` ON users.userID = runs.createdBy
    LEFT OUTER JOIN `user_run_times` ON user_run_times.runID = user_runs.runID 
    LEFT OUTER JOIN `run_favourites` ON run_favourites.runID = user_runs.runID
GROUP BY
    user_runs.runID,`createdBy`,`username`,`dateCreated`;


You will need these indexes

ALTER TABLE user_runs ADD INDEX userID_runID_ndx (userID,runID);
ALTER TABLE runs      ADD INDEX runID_createdBy_ndx (runID,createdBy);
ALTER TABLE runs      ADD INDEX createdBy_runID_ndx (createdBy,runID);