Putrajaya is an upscale resort area about 45 mins. from Kuala Lumpur, and was developed as such by the Malaysian gov't. to attract foreign investment and tourism. It is a very nice place to chill for a few days enroute to Thailand if you just want to be cocooned in luxury for a few days ... and at very affordable prices.
Kuala Lumpur is an interesting place - a beautiful city with a lot on offer, including easily arranged day trips to the surrounding countryside catering to whatever interests you.
Singapore would indeed be a great choice if you've not already been there. It's probably the cleanest and most well ordered country on earth. It's more expensive than KL, but there's a lot of history there to distract you from shopping excursions up and down Orchard Row.
If you're flying from the US you might consider Tokyo, Seoul, or Taipei as stopover points on future trips. Given the Great Circle routing by the major carriers going to Bangkok they wouldn't be too far out of your way, and all are fascinating places to visit.