Some have speculated that Tony Wonder or Pastor Veal locked the compartment in the cave. I'll throw out few other ideas.
Lucille 2:
Means: In the adoption story photo with Perfecto Telles (seen in Borderline Personalities and Off the Hook), Lucille 2 is shown with a cross on her necklace that appears identical to the cross that GOB found in the cave. I believe it's the only time a cross of that size and color shows up in this season. Although this doesn't mesh well with the timeline: the trick was committed in 2006 and Lucille 2 adopted Perfecto after she was running for election. Still, she could have replaced it.
Opportunity: GOB created his Christian magic act in part to compete with Tony Wonder's gay magician act. Tony Wonder's gay magician re-branding was funded by money stolen from Lucille 2 by Sally Sitwell. While this implies that Lucille 2 was unware she funded the act, it does establish a connection between Lucille 2 and Tony Wonder. Perhaps she got Tony to lock GOB up or obtained a Tony Wonder mask.
Motive: Lucille 2 arranged for Buster to miss the trial so that Lucille Bluth would be found guilty. She may have arranged for GOB to miss the trial for the same reason. We should also consider Lucille 2 had a sexual relationship with GOB, and him getting married would have hindered her from rekindling any future relationship.
Sally Sitwell:
Means: Could have stolen the cross from Lucille given she stole $100,000 from Lucille Austero. Given the timeline, Lucille 2 may have replaced if it was stolen.
Opportunity: She could've obtained and worn the Tony mask (would easily fit with her alopecia).
Motive: Wanted to crush the competition given the money involved in the re-branding.
GOB:
Experience tells us GOB causes his own magic show goofs.
Are there any other clues or ideas out there?
Update: Some other pieces of information that some people may have missed. When GOB is first on the cross, there's no message on it, but after he's taken down, there's a "Love Each Other" banner on it. The cave is hidden under a big sheet before GOB is taken down from the cross. According to the narrator, "it very clearly said in the centurions' script to ignore the magician's protests." When the GOB dummy is unwrapped, there are two dead doves, a note saying "If I have not yet returned, I am in the Rapture," and the back of the "Shhhh!" sign says "Love Each Other" ("Love Each Other" is written in cursive, "Shhhh!" is not). When GOB first finds the cross in the cave, the "And As It Such, So Also As Such Is It Unto You" music plays. At the model home, GOB tells Michael, "Tony Wonder was there in the cave the night that I did my big illusion." At the Gothic Castle, Tony Wonder tells GOB, "Your assistant probably sabatoged you."
There's a remote chance Ann's pregnancy is related. It's implied GOB is the father. At the model home before the wedding, GOB tells Michael "my diet has become insane and this Jesus character, I mean, he was shredded. Meanwhile, we have sex one time, and then she's just, you know, over it. Lets herself go. Her stomach's out to here." If GOB is the father, it makes his first conversation with Steve Holt a lot more ironic. However, it also makes Ann's behavior really confusing.