Depends on your budget. There are a lot of options out there. If you are a modular (from your avatar it looks like you are a 99-04 car) you can do anything from a built T-5 to a Magnum on the high end or a stock rebuilt T-45 or 3650 on the budget end. If you are just doing a basic replacement I'd do a good rebuild of whatever transmission your car came with to keep it simple although the only thing you really have to change when going from a T45 (99/00) to a 3650 (01-04) is a shifter change. For a T-45 hit up Zak at T45source. For a 3650 get ahold of Stan at Pro-Force Performance. For a built T-5 (A5) or Magnum get in touch with Tony at Astro Performance.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.