Popularity of such fanfiction can vary. It depends on factors like the quality of writing, how well the author develops the relationship between Shikamaru and Sakura, and also how much it appeals to the existing fan base. Some fans might be really into seeing this unexpected pairing explored in detail, while others might be more focused on the traditional pairings from the original series. So it's hard to say which ones are popular without actually searching through the fanfiction archives.
I'm not sure specifically which ones are extremely popular. But on various fanfiction platforms, there are likely many stories with this theme. You can search on platforms like FanFiction.net or Archive of Our Own to find out.
There could be some popular 'shikamaru likes sakura fanfiction' if there is a large enough fan base interested in this pairing. It might be that some of these stories gain popularity because they offer a fresh take on the Naruto universe. Writers might explore different aspects of their relationship, such as how they handle conflicts together or how they support each other in achieving their goals, which can attract readers.