Okay, for the last time I am going to summarize the different ways Jenova was released from the Shinra building, and explain which seems the most logical.

(1) A successful Sephiroth Clone or a manifestation of Sephiroth released Jenova. This seems to be an okay explanation because Palmer says "he saw Sephiroth with his own eyes".
Flaws:
(a) There is no explanation given as to why this exact time was chosen for the clone to release Jenova. Also, why the heck would Shinra allow a successful Sephiroth clone to run free? Don't you think if Hojo created a successful clone, Shinra would use that clone to their advantage? And even if Jenova took control of this clone, there's never any mention of a clone that escaped. And I think something as big as that happening would not be able to remain behind closed doors.
(b) Why is Cloud's cell open? Someone suggested that Jenova/Sephiroth could be a valuable asset, so they released Cloud while killing all the other Shinra soldiers. Okay, so how did the Sephiroth clone know that cloud was in that cell? Is the clone psychic? Not only that, why wouldn't the Sephiroth clone kill the other party members in the other cells, or at least kill Tifa? Jenova has no mind control over them, so why would she need them alive? She doesn't, which means that neither Jenova or the Sephiroth clone opened Cloud's cell. Also, the explanation that Cloud's cell was simply opened to advance the plot or so we wouldn't die of boredom in a video game is a weak and unacceptable answer. You could answer many questions in Final Fantasy VII with "cuz it's a video game and it doesn't have to make sense."

(2) Hojo released Jenova from the cell. The way in which the cell was opened pretty much answers this question, unless Hojo went on a spaz attack and trashed the door. I'm sure somebody would notice though.

(3) Jenova broke free from the cell. In my opinion, this is the second most probable. When Cloud looked into the cell, Jenova communicated to Cloud or something to that extent(the seizure Cloud has). Maybe this interaction between them brought Jenova back to a conscious level and thus escaped.
Flaw: Read (1)(b) above. Still no explanation as to why Cloud's cell was opened. Whether it be a Sephiroth Clone or Jenova, the other party members would have been killed.

(4) Cloud released Jenova from the cell, with Hojo releasing Cloud from the prison cell. Unlike the other theories, this one has no flaws. The pieces of the puzzle fit well for this theory. Jenova communicated with Cloud, commanding him to release her. Hojo unlocked Cloud's cell, curious to see whether or not Jenova still had control over Cloud. Cloud, not mentally stable and not in control of his actions, unconsiously uses his sword to slash open the tank and release Jenova, kills other soldier's in the process. Jenova takes on the form of Sephiroth, and murders President Shinra. Hojo leaves Shinra to avoid suspicion in an extremely messy(and debatable) matter.

Now, I await my opposition.........