The case doesn't actually seem open and shut at all. CL seems to have a "moral high ground" in that they provide the original service and the platform for users to post information, but the legal ground is more shaky. It is relatively settled in copyright law (which appears to be the main thrust of CL's argument) that effort alone does not award copyright protection[1] (or indeed, any property rights in general[2]).
For example, phone listings are not copyrightable, nor is news. The general question is whether there was creative expression (which can include 'creative' presentation or organization). If I were Padmapper, I would argue that classified listings are just a collection of facts, in which case they are not copyrightable. Padmapper does not actually use the listings directly, but extracts the information and puts it in a different format (their interface). On this point I think their case is relatively strong.
Where CL might be able to make a better case is their TOU. The TOU forms a contract between CL and their users. In almost all such prominent cases, this type of contract has been found to be enforceable[3]. If this line of reasoning is followed, then Padmapper will probably lose on this point because they agreed not to "copy, aggregate, distribute", etc.[4]
If this is a contractual claim the damages would be what CL could have expected if Padmapper had not 'breached' the contract - in this case I'm not sure that amount is particularly large, because Padmapper redirects to CL's site for the actual listings.
TLDR: copyright claim seems weak, but the contractual claim might succeed. The trademark stuff seems like a red herring and is CL throwing stuff at the wall to see what sticks.
[EDIT: see below, I overlooked the fact that Padmapper is no longer using CL data directly, so they might not be bound by the TOU at all. Same goes for 3Taps since they use Google's cache. Looking stronger for Padmapper]
[1] Feist v. Rural, http://en.wikipedia.org/wiki/Feist_v._Rural
[2] INS v. AP, http://en.wikipedia.org/wiki/International_News_Service_v._A...
[3] http://en.wikipedia.org/wiki/Clickwrap
[4] CL Terms of Use (see section 3), http://www.craigslist.org/about/terms.of.use