Pretty sure most people are aware you don't have to use iTunes to use an iPod. I do, I love iTunes. Don't see why you wouldn't want to use it.
Yeah, depending on the model you have 1, two, maybe 3 other choices
http://en.wikipedia.org/wiki/Comparison_of_iPod_managers virtually nothing is a full-featured replacement, only a handful support transferring music to an iPod Touch/iPhone. So, yeah, I think it is a fair statement to say that there aren't any real options beyond iTunes, especially for the latest models of all iPod products, and support is hit-or-miss as far as other models and supported features.
On topic: The OP needs to ask himself one question: do you really want thiose few apps enough to warrant the vastly higher price-tag associated with the iPod Touch in comparison to other PMPs (including even older iPod models)? If those apps are THAT much "Must Have!" then you obivously have already made your decision, if you are any less certain, you are probably better off saving your wallet the pain and getting a cheaper PMP.