Black Books and Spaced are proven to exist in the same universe, since in one episode of Black Books, Manny is heard talking to Twist Morgan. Because of this, the only reasonable explanation for why Bilbo and Manny (both played by the same actor, Bill Bailey) look so similar is that they are identical twins. Additionally, Tim is probably related to Evan, the manager of Goliath Books, and Howell the shipping forecaster could be Duane's slightly deeper-voiced cousin.
Spaced is an alternate reality where 2000 AD's non-Megazine Spin Offs (Crisis, Revolver, etc.) succeeded and they were able to form a company of their own when they parted from Fleetway (as opposed to being bought by Rebellion, as in Real Life). A copy of 2000 AD is seen on Damien's desk and Tim's ambition is to work for Darkstar, even though he is established In-Universe to be a huge 2000 AD fanboy. Ergo, Damien Knox is Tharg.
Mike and Tim's robot, Private Iron, has 'TFU' painted on it, which stands for 'The Fuckest Uppest'. This implies that a previous version of Private Iron (or a previous robot) was labelled 'The Fucker Upper'. Taking that further, the first generation could have been 'The Fuck Up' and represented something of a disappointment.