Here is my current dilemma: I used the data from MSX6 Survey and want to put a citation or some kind of acknowledgment but I can't seem to find any concrete paper or reference text to put in the paper. Any of you would know what paper to cite?
The appropriate thing to do is cite the catalog itself. Here it is in the ADS: "MSX6C Infrared Point Source Catalog. The Midcourse Space Experiment Point Source Catalog Version 2.3."
The preferred format in the usual ApJ style is "Egan et al. 2003, VizieR Online Data Catalog, 5114, 0", but ADS can give you the BibTex too.
Finally, note that the MSX people ask that you include the following acknowledgement in your paper (something which you don't strictly need to do, but which is nice):