The modern way to get untraceable money (according to [1]) is to set up (legitimate) small companies, then wildly overcharge the government for services.

Looks like your standard government incompetence and passing cash to well connected friends, and doesn't show up in any sort of government black budgets accounting.

The author estimates that one Western intelligence agency has over 2,000 such companies.

Fun fact: should one of these companies actually end up profitable in the course of its legitimate activities, it then gets overcharged by the unprofitable ones.

[1] http://www.amazon.fr/Missions-methodes-techniques-speciales-...