This is the list of 50 such search engine ranking factors. These is the list which came to my mind right now. I may have missed on some of them. So, if you know of any and can add to the list, please comment it. I will add it in the list.

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50 Search Engine Ranking Factors
1. Keywords in the title of the page
2. Keywords in the headings of the page (h1, h2, h3, etc.)
3. Keywords in domain name
4. Keywords in the file names of the pages, images or any other content
5. Keywords in bold, italics and underlined text
6. Keywords in alt text for the images
7. Keywords in the text of different color/size
8. Variations of keywords on the page (Eg: eat, ate, eaten, eating, eater, etc.)
9. Keyword density on the page
10. Appearance of the keyword in the above half of the page
11. Keywords in the description meta tag
12. Keywords in the keywords meta tag
13. Uniqueness of title, description and keywords with other pages of the site
14. Age of the domain
15. Age of the page
16. TLD of the domain (Eg: .in domains will rank better in google.co.in domain)
17. Hosting location
18. Pagerank of the site
19. Quality of the content (well written, informative, not duplicate)
20. Number of backlinks
21. Quality (PR) of the backlinks
22. Anchor text used for the backlinks
23. Title text (if any) used for the backlinks
24. Age of the backlink
25. Where the backlink appears on the page (top of the pages, bottom of the page)
26. Is the link in-content or exists with other links (pointing to some other site and separated with some specific text [like “,” or “|” ])
27. Number of total links on the page which is linking to you
28. Is the theme of the linking page is same as the linked page
29. Relevance of the keyword with the primary subject of the overall website.
30. Website load time (server response time and the size of the page)
31. Availability of the server (those 99.99% uptime things)
32. Outgoing links (to whom are you linking? Are the related?)
33. Number of pages in the site
34. Website navigation and accessibility (reach-ability of all the pages easily)
35. Links to the internal pages (yes, this will improve the ranking of the main page as well if the navigation is correct)
36. How many people come back from the site to the search engine after searching for the keyword (my be Google tracks this with toolbar)
37. Number of internal page links on your pages (not more than 100)
38. Number of external links on your pages (try to minimize)
39. Backlinks from .gov, .edu links (some thinks, its not a factor)
40. Using “-” hyphen (and not “_” underscore) in your file names wherever space is needed.
41. How often the site is updated
42. Duplicate content from other sources (negative effect)
43. Linking to bad sites (called bad neighborhood) (negative effect)
44. Keyword stuff on the pages or over optimization (negative effect)
45. The speed by which new links are building up for a site. Is it consistent over a longer period?
46. Backlinks from DMOZ and Yahoo directory are considered quite valuable.
47. Avoid session identifiers (SID)
48. Deletion of the pages (dead links on the site) without proper 301/302 redirect (negative effect)
49. HTML validation of the document (I am not sure how much effect it makes)
50. History of the domain (did it do anything bad in the past?)

Did I missed on something? Add them in the comments and I will add it here.