Because someone wanted this: a list of aircraft investigation resources.
First thing: you always need to be able to map registrations to aircraft serial numbers (MSNs) and vice versa, as well as linking registrations to operators and vice versa. So you need to subscribe to one of several commercial databases that provide this information. Otherwise you'd have to follow up each registration individually with the state of registry, which isn't so bad if it's the US (you can query the registry at faa.gov) or the UK CAA's G-INFO. If it's Equatorial Guinea or Kyrgyzstan, though, it won't be available online or really at all, and that's just how the registrants want it.
I use ATDB, but there are others - the biggest one is Airclaims, which is marketed at insurers and debt chasers, but it's seriously pricey.
You'll also often want to find out where an aircraft was at a particular date, and if the registration and operator on file matched with the reality. Fortunately the world is full of volunteer spies, plane spotters, who take enormous numbers of photos of anything that might fly and post them on web sites. This is how German Amnesty managed to characterise the CIA rendition planes. Airliners.net is the biggest and has a full-featured search engine, but JetPhotos and a few others are worth trying if you turn up a blank. ATDB will try to pull photos from various servers matching your current query. Try querying by registration as well as MSN, and note that if you know the exact type (all six digits of a Boeing designation rather than just 737) you can often do a type-at-location search.
A lot of airports publish their movements on the web - this is why I did the Viktorfeed, to automate watching Dubai and Sharjah airports. This is useful if you want to know who is going where, or who's recently been where, and you may be able to find out more by cross-referencing. For example, if Airline X's flight from Dubai to Baghdad is listed as a passenger flight with a 727 and they only have one 727 with a pax, combi, or quick change configuration, you've got the registration and possibly the MSN.
Also, for some parts of the world, you can monitor Air Traffic Control data through sites like FlightTracker or FlightAware and LiveATC. A lot of these are aggregators for people who operate "virtual radar" devices, which receive the SSR transponder data practically all aircraft squawk when they hear a surveillance radar. Here's an example. The problem is, of course, this depends on owning fancy radio equipment being tolerated in the places you're interested in. If your BlackBerry is considered subversive, or there's just no electricity, you're unlikely to find a virtual radar server - and they won't work if there's no radar coverage. (However, if your staff go somewhere weird, why not...)
The Aviation Safety Network website provides a database of accident reports, which can be useful. AirNav has a huge database of airports, although most of them are on Wikipedia. There's a lookup site for ICAO and IATA codes here. The Great Circle Mapper is a useful calculator for ranges and routes and makes pretty maps. Obviously Google Maps and Earth are useful if you're planning more complex visualisation.
Things to look out for: networks of companies that repeatedly trade the same aircraft, especially if they're based in the same location and their corporate registration is somewhere else and bizarre. Inconsistency. Unlikely details (the office that is in Kiev and is a cinema, the manager who is a Soviet ice hockey player and is dead). Things you can't easily find: details of the cargo or whoever eventually controls the company.
Also, do be sceptical and don't turn yourself into Evan Kohlmann (via Patrick Lang - check out Adam Silverman's thoughts in the comments).
I can remember when the Emerson & Kohlmann show sounded fresh and new in late 2001. I can also remember when the Counterterrorism Blog launched and turned out to be really just a lot of drum-banging rightwing propaganda and some really quite horrible guilt-by-association games. Worry about the false positives.