I always start by checking for a Kindle version. If there is one, then usually it is also available as a MOBI. However, since the Kindle version is only available to Kindle owners, the downsides to this are that sometimes there is only a Kindle version and often the Kindle price is less than at other sites.
There are only two DRMed MOBI wholesalers, so checking mobipocket.com and
OverDrive should find all DRM-infested MOBI ebooks (I'm not sure if there are overdrive exclusive MOBIs, so checking mobipocket.com may be sufficient). Note that mobipocket.com always shows the list price, and so is almost always more expensive that other sellers of MOBI ebooks.
This approach can miss DRM-free ebooks, which is a shame since DRM-free is best. A few publishers have their own DRM-free sites (e.g. Baen), but FictionWise has the largest selection.