Here is a list of recommended Flash games compiled by the clysm himself, developer of the fan-favorite 2D platformer Seiklus. The selection is alphabetically ordered, as all good lists should be.

(clysm is currently working on the exploration game Avaus and putting the finishing touches on Velella, his collaborative project with darthlupi.)

Another list of recommended indie games can be found in this forum thread on CAG, where the current discussion is centered around a couple of free and commercial releases that anyone can download to get a feel of how much indie games have improved over the years.

Flash Games (autofish.net)
General Indie Gaming Thread (CAG)