Microsoft might have taken that functionality away from us in what concerns Master Pages. But… they have not taken it away when it comes to page layouts. You can insert web parts in a custom page layout.
The main con about this approach is that if you need those web parts available to all pages being created on your site, then you have to create a copy of each page layout available out there and insert the web parts to all of them. So when your customers create new pages, the web parts are going to be there. (By inserting them once in the MOSS 2007 master page you were done; now you have to replicate the job for all page layouts for which you want those web parts to display.)
Note: As I always emphasize, make sure you are working on a copy of Microsoft’s originals and leave the originals from Microsoft alone.
This is what you need to do:
2. Insert the web part at any web part zone on the page (it doesn’t really matter where since this is more of a placeholder until you are done creating the web part completely). In the case of custom Content Query Web Parts, do all of the necessary customizations to the web parts, style sheets, CSS rule sets, etc.
3. Download the web part or web parts to your hard drive;
4. Upload the web part or web parts to the site’s Web Part Gallery;
5. Using SharePoint Designer, open your custom page layout
6. Go to the location of the page where you would like to insert the web part (it could be a row or cell in a table or a <div>); I usually work in split mode. You may want to use the Code or Design view; it’s up to you and whatever it is easier for you.
7. Select the Insert tab on the ribbon and then select Web Part within the Web Parts group;
8. SharePoint Designer will display a Web Part drop-down menu; locate the web part uploaded in step 4 above and insert it in your page;
9. Save, check in, and publish the page;
10. Go back to your site using Internet Explorer this time (not Designer) and create a page using the modified page layout. Or if you have already created a page using this particular page layout, open it. Make sure the web part is now displaying at the desired location on the page.