Jason,

The best HO Union Pacific boxcars (40', single door) IMO are from Trix/Marklin.  Their UP 40' double door is a very accurate model, but has the wrong lettering for this class of car - see Speedwitch's site for decals and information on how to correct the lettering.  Trix/Marklin also made nice UP hoppers and CA-3 cabooses.  All of them are a bit pricey on eBay, but patience can be rewarded in searching for lower priced auctions.  As for boxcars for the other RRs you listed, IMWX/Red Caboose and Intermountain cars and kits are pretty accurate representations for most of them, although some on this list would have the models be more accurate (more accurate doors and handbrakes, for example) - watch for postings by Andy Carlson about his offerings.

Red Caboose made great HO UP GS gondolas, and the real ones were used for hauling many things including coal to UP engine terminals and probably ashes out.  They are available as kits occasionally on eBay and RTR from Intermountain.  Intermountain also offers 1958 cuft covered hoppers which are gems.

I hope this helps.

Todd Sullivan