The biggest insider trading prosecution in two decades still would not be more than a one- or two-day story if it wasn’t for the criminal charges against hedge fund titan Raj Rajaratnam.

For all the talk about disposable cellphones, bags of cash being delivered to tipsters and people with nicknames like Octopussy and the Greek, nearly all of the 20 defendants in this case appear to be nothing more than typical low-level Wall Streeters working at dime-a-dozen day-trading shops.

The characters are colorful and their alleged activities are the stuff of movies, but they are not Wall Street luminaries. (For a graphic illustrating the case, click here.)

Even as prosecutors boast that this investigation is shining a bright light on some of the hedge fund world’s most tawdry practices, federal authorities still have not charged anyone of real stature outside of Rajaratnam.

It’s clear, however, that prosecutors would like to do exactly that, which is why this investigation is far from over. It’s also why hedge fund managers and their investors have reason to worry about where the next shoe may drop.

The cooperation agreements from the five people who’ve already pled guilty to various counts of insider trading read like a warning shot to others on Wall Street. While the court filings don’t name any names, and identities of potential co-conspirators are shrouded behind references like “a portfolio manager for a certain hedge fund,” it is clear investigators have put together a list of people they suspect of wrongdoing.

In particular, the cooperation deals signed last month by Ali Far and Richard Choo-Beng Lee, as well as the criminal complaints filed against them, make a nice roadmap for where prosecutors would like to take this investigation.

Far, a Galleon alum, teamed up with Lee in 2007 to open Spherix Capital, a short-lived tech-focused hedge fund that authorities say was a hotbed of insider trading activity.

In Lee, it would appear prosecutors would like to build a path right to the doorway of Steven Cohen’s SAC Capital, a $12 billion behemoth and one of the world’s best-known hedge funds. As part of his deal with prosecutors, Lee has agreed to tell authorities of any insider trading he may have done while working as tech analyst at SAC Capital from 1994 to 2004.

Now that’s not to say Lee has told prosecutors he engaged in insider trading while at SAC. And there’s nothing in the agreement that suggests Cohen did anything wrong, or anyone at SAC Capital was aware of any potential wrongdoing by Lee.

But it appears that prosecutors want to find out if something bad went down at SAC Capital when Lee worked there.

A spokesman for Cohen and SAC declined to comment.

But Lee may provide prosecutors with more than a view into SAC Capital. In a criminal complaint, authorities allege that Lee conspired to engage in insider trading with portfolio mangers from at least four unnamed hedge funds other than his own Spherix.

The other hedge funds are not identified in the complaint. Galleon, however, has been at the center of the case. Three other funds have also attracted scrutiny.

Stratix Asset Management was where Lee worked before Spherix. S2 Capital Management is where Steven Fortuna, one of the cooperating witnesses in the case, worked. And Quadrum Capital’s founder has received a subpoena in the case, according to the Wall Street Journal. Quadrum, which shut down before the Galleon case broke, recently retained Kevin Harnish, a lawyer who specializes in securities enforcement cases.

Far may also prove a pivotal prosecution witness in building the case against Rajaratnam. Court filings suggest Far, a one-time top lieutenant to Rajaratnam, may have engaged in insider trading as far back as 2003 — a time he was still a tech portfolio manager for Galleon. If that’s true, Far’s testimony could be highly damaging to Rajaratnam at trial.

The suggestion Far wheeled-and-dealed in confidential corporate information for nearly six years may draw added scrutiny to a number of private partnerships he formed in Texas in August 2004. The partnerships set up by Texas attorney Todd Amacher appear intended to have been used by Far as investment vehicles.

Amacher, as I previously reported, set up similar partnerships for several other hedge fund managers, including a tech analyst who later went to work for Far’s now-defunct Spherix, and a portfolio manager with Fir Tree Partners.

Now there’s no indication prosecutors are looking into any of those partnerships, or the hedge fund managers behind them. But in this environment, when prosecutors are leaving no stone unturned to catch a big hedge fund fish, nothing may be beyond their purview.