The latest release is Version 1.40 Linux release A, based on the brand new 1.40 core. You get these changes from PR #5:
Linux

- XML ROM support
- Archive browser comes up automatically if you select a zip or 7zip archive with multiple NES files in it
- Option to select favored console
- More flexible video configuration including OpenGL hardware scaling
- Input mapping in the GUI
- Core logging is now enabled to the terminal you start NEStopia from for easier diagnosis of problems
- Cheat Manager with flexible support and import/export capability (.xml cheat files will interchange with the Windows version just fine)
- Automatic soft-patching added
- Coin inputs added for Vs. system
- Audio filters added for fun
Core (includes changes from 1.38, 1.39, and 1.40)

Additions:

- ROM sets and external database support using new XML format co-developed with Bootgod.
- Mapper 36, 103, 104, 106, 120, 126, 175, 176, 223 and 224. Info from mad dumper, CaH4e3 and Temryu.
- UNIF boards GS-2013 and BS-5. info from CaH4e3.
- Emulation of bus conflicts for certain boards.
- Database entries.
- Core API documentation in HTML through cppdoc.
- UPS patching format support.
- Database lookup on soft-patching.
- Database entries. Info from Bootgod.
- More recognized boards. Info from Bootgod.
- Preliminary Dendy console support. Fixes Magistr (Subor) and some other ‘clone exclusives’. Info from Flamer and HardWareMan.
- DMC DMA read conflicts. Info from blargg and bunnyboy.
- Mapper 177, 179, 219 and 221. Info from CaH4e3.
- Database entries.

Changes:

- PPU power/reset timing and register states. Info from blargg.
- Misc IRQ/NMI/BRK/DMA special-case behavior. Info from blargg.
- NTSC/PAL switch during emulation will now force a hard-reset.
- Misc mapper emulation improvements. Info from Bootgod.
- NES-EVENT board timer more accurate.
- Board names. Info from Bootgod.
- Refactoring and mapper codebase overhaul.
- Speed optimizations (accuracy NOT compromised!).
- Mappers 21, 23, 25 and 185 no longer supported using plain iNES
files because of format restrictions.
- FDS saves through UPS instead of IPS.
- Database entries. Info from Bootgod.
- Refactoring.
- Better and more flexible PPU address line implementation at the expense of some speed.
- Database entries.
- Refactoring.

Fixes:

- MMC3 soft-reset IRQ bug.
- Database entries.
- FDS file saving bug.
- NTSC burst phase incrementing bug.
- Potential memory leak in database loader.
- UTF16 to wchar_t portability fix in XML parser.
- Const-correctness bug caught by GCC 4.0.
- Wrong palette sometimes when switching to/from VS images.
- Wrong image information sometimes, e.g. battery when there isn’t any.
- Save state NTSC/PAL mode saving.
- Minor save state inaccuracy fix with tape recording.