Organize your strips. For story-based webcomics, your order is pretty much set, but for gag strips or those with various mini-arcs that are not dependent on a strict timeline, feel free to group your comics into sections with common threads. Group any filler art or sketches you want to include into their own section. Fix any spelling mistakes or art errors that you may have overlooked when you first published the comic strips on the Web.
Evaluate how many comics you will be printing and how they will fit on the pages. To do this, make a list, section by section where applicable, of the comic title, the date published and the size of the comic. The Web gives us a lot of flexibility in how we structure webcomics, but this can backfire when we try to print on standard-sized pages--so measuring each will be a start towards resizing and arranging them for the book.
Take a preliminary count of your pages. Online comics in a 4:3 ratio can easily go 2-up per page, whereas square or vertical strips will fit better on their own pages. A standard 3 to 5 panel newspaper-style strip can be printed 3 or 4 per page. This is probably not going to be your final page count, so don't worry if this seems low at first.
Create some additional content. This "value added" concept makes your print collection all the more enticing since this content will only be available in print, unlike the majority of your work that is available free, online. Strips that you drew but didn't post, thought of but never drew, pages from your sketchbook and sketches done by request are all excellent ideas for additional content. Add these to your lists and working page count.
Scan in any work that isn't currently digital and clean it up per your usual process. Make sure all images are at least 300dpi for maximum quality; if not it's best to rescan than try and increase the resolution from low to high. Import your files into a page layout program and start composing your pages.
Include the other non-comics pages that all books should contain. The Title page comes first, followed by the Copyright page which frequently falls on the back side of the Title page. A Table of Contents is great (especially if you have divided your book into chapters or sections), and then would be followed by an Introduction or Forward (which can be something very similar to your "About" page from your website).