which one to choose?

[KnottedYet]

Are you looking for new bikes or used ones?

Or both?

New, I always recommend the Kona Smoke ($350) or Kona Dew ($400). I'm pretty boring and predictable that way. (Smoke is an awesome commuter. Just saying...)
Used, anything that feels good and meets your budget! Girly-looking bikes are less likely to be stolen, but that's no guarantee of safety.

If you have a Bike Kitchen or Bike Works or other bike-assistance program near you that sells refurbished bikes to fund their program, I'd definitely look into that! http://forums.teamestrogen.com/showthread.php?t=24656

[Blueberry]

Could you get a folding bike, and take it inside with you? That's probably the safest way to go. Otherwise, I use a mini U around the rear wheel *inside the triangle* (see Sheldon Brown's locking explanation), and separately cable lock the frame and front wheel to the rack. I take all computers, etc. inside with me.

As far as panniers, it depends on whether you will be a fair weather commuter or an all weather commuter. If the former, I really like the plain grocery bag panniers - just dump stuff in and go. If the latter - ortlieb stuff and arkel stuff rocks.

Good luck on the job!!!

Edited to add: Many ebay bikes are stolen too. The key, I think, is to talk to the seller. When I've sold bikes on Craigs, I've been willing to provide at least a copy of the original purchase receipts, and my shop guys can vouch for me...

CA