Each Yu-Gi-Oh! anime series has a different kind of eyecatches, although they are usually replaced with different graphics in the dubbed version, and removed in some international dubs.
Yu-Gi-Oh! (Toei anime)
The first anime series' eyecatch for the begin of the commercial break shows the Millennium Puzzle, which then shatters, and Yami Yugi's silhouette appears with the series' logo beside him. The eyecatch for the end of the commercial break shows the series' logo with the eye of wdjat over it; Yami Yugi's silhouette then appears from underneath, more zoomed in, and inside it a wall with Egyptian hieroglyphics is seen. Then, the background also changes to the wall, and a fissure in the eye of wdjat in the wall is zoomed in, and the episode resumes.
Yu-Gi-Oh! (NAS anime)
Yu-Gi-Oh! GX has two different sets of eyecatches; all of them show the characters who were most relevant in the episode, usually the characters who Duel in it, sometimes with their main monster shown in the background. In the beginning, the first eyecatch showed one character, and the second, the other one. Later, starting on season 3, the first eyecatch was skipped, with the Yu-Gi-Oh! GX logo being shown in the down right corner instead, and the second one shows both characters (more than 2 sometimes).
Yu-Gi-Oh! 5D's too have 2 different sets of eyecatches, although they didn't change from episode to episode. The first set was used for seasons 1 and 2, and showed Yusei Summoning "Junk Warrior" (the first one in a Ground Duel and the second one in a Turbo Duel). The second set was used from season 3 to 5, and showed two shots of Yusei with "Stardust Dragon" (also in a Ground and in a Turbo Duel).
Yu-Gi-Oh! ZEXAL doesn't have an eyecatch animation. Instead, its logo is shown in the bottom-left corner at the start and end of the commercial break.
- Eyecatch on Wikipedia