The Eighth Doctor‘s timeline is the most open to interpretation given all we know is one TV story and that he is in some ways the bridge to the new TV series from the Classic. To set out the sequence I will use the rule of ‘follow the companion’ (and the wiki entry - update October 2012: deleted). For the odd story when the Doctor appears without a companion I have to assume that they slot between sequences.

This means that from a BF (and now also novels as I read them - characters in italics) point of view the main companions are:

1. Alone
2. Samantha Jones (blonde) [also a diversion, not recorded to Stacy and Ssard]
3. Alone (whilst looking for Sam)
4. Samantha Jones (blonde)
5. Samson and Gemma Griffin
6. Mary Shelley
7. ?Back to Samson and Gemma?
8. Charley
9. Charley and C’rizz
10. Charley
11. Alone
12. Lucie Miller
13. Alone
14. Tamsin Drew
15. Lucie Miller
16. Alone
17. Molly o’Sullivan
18. THE TIME WAR.

I ignore the other Company of Friends companions as I don’t have the background in them!

Since writing the above I have been dabbling into the EDA novels and (ignoring canon) will work them in, I have no plans to integrate the various comic strips!

Update August 2012 - Big Finish have introduced a new companion Molly o’Sullivan as mentioned here.Logic

We know he appeared in The Movie (my review here) and then ends up alone. He travels with Gemma and Samson Griffin who I would normally ignore except that Big Finish bind them in the story Terror Firma. Having written that they are now linked back in the Mary Shelley story The Silver Turk.

From wiki Mary Shelley is next (skipping the novel characters) then Charley, post Zagreus we get C’rizz for a while then are left with only Charley again.

Later we get Lucie (the BF publication order being the chronology according to BF). When Lucie leaves there is a patch (for Earthly Child?) where he is alone, then we get the fourth series shuffle of Tamsin then Lucie then nobody.
I should probably drop Susan in here as well.

From the Ninth Doctor we know there is a Time War and out belief is that this is how the Eighth Doctor bows out. This is a ‘Here be Dragons’ part of the chronology which will only ever (or so it seems) be inferred.

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