Over the past year I have gathered a handful of loose MVS carts for my collection without really knowing whether they are legitimate or not. I was hoping for a steer from those in the know of what I should be looking out for as indicators of a bootleg.
This helps for starters: http://www.neo-geo.com/forums/showthread.php?120255-The-MVS-Bootleg-Forensic-Thread
http://www.mvs-scans.com/index.php/Main_Page That is a god send! Great for checking you have legit boards. Generally eproms are bad in MVS, but not always of course. Generally the chips should have the NGH number on them (see here for list of NGH numbers http://www.neo-geo.com/snk/masterlist.htm). Usually there should be no wires on the boards, although bear in mind official repairs will have them and some versions of certain games do as standard. (My Garou is the same as set 2 for example http://www.mvs-scans.com/index.php/Garou:_Mark_of_the_Wolves) For labels (and cart shells), well I have no hard and fast rules myself, nor a site I know of to direct you to, that has definitive answers. NG.com has lots of helpful members who can assist though. If they are the glossy / shiney style with serials you should be ok. If they have serials cut out they are usually ok (as that can historically have been arcade ops selling them on but removing the serial to avoid a trace back to them). Generally you can get a feel for them if you have a few carts. As you mention you have loose carts I take it you're not too fussed about artworks / boxes etc.
