It's tough to pick out good episodes for this show, because they very often try to weave together two or three plotlines and it's very seldom that they're all funny. Here's ten that are worth watching (in series order):

World's Greatest Couple: Lily moves into Barney's apartment
Slap Bet: Robin's mysterious past is blown wide open
Spoiler Alert: Marshall awaits bar exam results
The Bracket: Barney tries to track down the woman who is sabotaging his sex life
The Fight: Ted and Barney get into a barroom brawl
The Playbook: Barney gets back into the swing of dating
Perfect Week: Barney dating, too
Rabbit or Duck: Barney still dating
The Bro Mitzvah: Barney's bachelor party
How Your Mother Met Me: what the Mother was doing all those years

Best overall episode is a tough pick, too. Maybe The Playbook or The Bro Mitzvah