Well, It sounds like it might be one of the u-joints on yours (my old YJ did the same). My '05 TJ just started knocking in the front passenger side, Im thinking its the u-joint but it seems solid with no play when I looked at it.
2005 LJ Rubicon 4.0L, NSG370 6-Speed Manual, NV-241OR, Impact Orange
2004 WJ Overland 4.7L H.O. 545RFE, NV247, Bright Silver
1995 YJ S 2.5L, AX-5 5-Speed Manual, NP-231, Bright White
Sold the TJ X for a LJ Rubicon... Good Deal!