Since the tag got deleted I'm collecting the stories that were formerly tagged with the "Time Skip" Tag. If you have saved any of them or can remember them, please post a link the the story. I've set up a public list where I will collect those stories even if the tag is gone.

http://dynasty-scans.com/chapters/the_heir_of_the_curse
http://dynasty-scans.com/chapters/love_1
http://dynasty-scans.com/chapters/boyfriend
http://dynasty-scans.com/chapters/prunus_girl_epilogue_prunus_boy
http://dynasty-scans.com/chapters/my_beloved_ch03
http://dynasty-scans.com/chapters/notes_from_the_garden_of_lilies_volume_2_special
http://dynasty-scans.com/chapters/ni_pukha_ni_pera
http://dynasty-scans.com/chapters/yearning_for_macaron
http://dynasty-scans.com/chapters/love_slave_ch08
http://dynasty-scans.com/chapters/fall_in_love_could_only_fall_in_love
http://dynasty-scans.com/chapters/gamma_ch17
http://dynasty-scans.com/chapters/im_a_fool
http://dynasty-scans.com/chapters/nijipuri_ch19
http://dynasty-scans.com/chapters/stream_will_tomorrow_and_the_warmth_in_your_hands
http://dynasty-scans.com/chapters/renai_manga_ch06#1
http://dynasty-scans.com/chapters/blue_flame_fragnant_clay
http://dynasty-scans.com/chapters/orange_yellow_the_proof_of_her_love
http://dynasty-scans.com/chapters/i_cant_tell_anyone_ch07

I dont remember if they were tagged as time skips, but after skimming a couple dozen of titles for a bit, these are ones I know have one.
http://dynasty-scans.com/chapters/unripe_fruit
http://dynasty-scans.com/chapters/secret_of_the_princess_ch06
http://dynasty-scans.com/chapters/ebisu_san_and_hotei_san_extras
http://dynasty-scans.com/chapters/hoshikawa_ginza_district_4_ch19
http://dynasty-scans.com/chapters/tender_night

I'd say the entire series of Clover sorta has the theme of Time Skips, cus the stories aren't told chronologically. Like, there's sisters of various ages and we're shown a chapter of their high school life, and it kinda goes back and forth?