Agents of S.H.I.E.L.D. - It's best watched in timeline order with the movies as the plots of each dovetail into each other (and make sure you watch at least the first season of Agent Carter before watching Season 7 of this show). If you're just getting started with the MCU, you may have to push through the first 12 episodes as the show doesn't really become regularly good until 1x13 (and doesn't become regularly great until closer to 1x17 or so).

Arrested Development - You can treat Season 3 as the final season or Season 5 as the final season. Arguments can be made either way as to which is preferable. Also if you do continue past Season 3, there are two different versions of Season 4 (and, naturally, arguments as to which version is better).

Battlestar Galactica - There are web series, movies, and a miniseries that are intended to be watched along with the show to give you the full story.

Brooklyn 9-9 - Season 8 starts out rough, but push through because the finale is worth it.

Cougar Town - Push through until you get past the Season 1 Thanksgiving episode and the show will slowly improve from there.

The various Defenders shows - Make sure you watch in release/timeline order. This is particularly important for Daredevil S3, The Punisher, and The Defenders.

LOST - There are various web series and videos to watch along with the show if you want the full story.

Runaways - Don't watch Season 3 until after you've watched Cloak & Dagger.

Scrubs - Season 9 is technically Season 1 of Scrubs: Med School rather than a continuation of the main story. Also make sure to check out the Scrubs: Interns web series between Seasons 7 and 8. And try to find a version of the show that has the original music rather than the streaming versions that have the original music stripped out.

Supernatural - Treat it as a five season show with a six season sequel show which has its own four season sequel show rather than one 15 season show. When you get to the end of Season 5 cut it off in the last minute or so when a lamp post appears. If you are satisfied with that as the ending, or you're a stickler for lore and continuity, treat that as the end of the show (but maybe track down a list of good later standalone episodes). If you don't care about lore and continuity and you want to continue seeing more stories featuring the main characters, proceed to Season 6. Then do the pause, reflect, and decide if you're happy with the current scene as an ending thing again in the Season 11 finale when there's a large shot of the sun. (You could arguably do this pause, reflect, and decide if you like that ending before proceeding for 15x19 as well.) Also, for Season 1 make sure you find a version that has the original music rather than the streaming versions where the original music was removed and replaced.