Latest one is pretty much standard by a large margin. Second would be news, and a distant third would be some kind of splash/cover that then leads into either a table of contents or the first page.
However, which option you choose should be based on your chosen format and update schedule.
The standard of having the latest comic on the front page works well if you update regularly several times a week or you have a simple strip format. However, if you update once or twice a week or slower, a news/blog page can sometimes be a better choice for the front page, especially if it's well-written and witty or insightful.
If you update sporadically in bursts, you might even consider something like a cover/welcome page that leads into table of contents (just a list of page numbers in brackets works well, especially if you highlight the latest batch of pages). Otherwise, people will think your comic is always dying or they'll be bugging you about when the next update is (or asking what your update schedule is, when you obviously don't have one).
Finally, if you add complete chapters with every update, then just go ahead and make a front page as a list of the chapters from newest to oldest, all of which lead into each chapter's first page. Then also have the date of each chapter's publication on the site directly under the link, so people coming back from a year or two ago (assuming you keep up the same project that long) can quickly figure out about where they left off. Thumbnail versions of cover pages can be useful for giving some visual cues on each chapter's contents and to help people find and remember chapters more easily.
