The list of native Linux/Alpha applications currently includes the following:
The Applixware suite of office applications, which has already earned some fame in the Linux arena, is now available for Linux/Alpha too: http://linux.applixware.com
Backup software is available from EST Inc (the personal edition of BRU is included with Craftwork Linux v2.2/AXP).
Microway sells Fortran compilers for Linux/Alpha. Information is available at Microway's home page.
Alternatively, there's a compiler from NAG. Linux/Alpha is just one of many platforms supported. Check out their home page.
Motif for Linux/Alpha is now available for free. Look around the various Linux software sites for binaries and source. Metrolink has also produced OpenMotif RPMs available for download.
MetroLink also produces a commercial X-server. If your graphics hardware is not supported by XFree, you may want to check out their homepage.
More and better sound-card support compared to what comes with the Linux kernel. Available from 4Front Technologies. Also don't forget to check out Alsa, the Advanced Linux Sound Architecture. They now have several Alpha machines and are ensuring that the next generation of Linux sound support runs on Alpha.
XVScan is, you guessed it, scanning software to use with John Bradley's xv. It supports "Most HP Scanjets, including the ancient ScanJet Plus..". Check out tummy.com, ltd.. (Thanks to Michael Champigny for pointing this out.)
Picture Elements's PCI image processing boards are actively supported under Linux/alpha. They also distribute some free software, including tools/patches that will help you crosscompile from Linux/Alpha for a variety of other platforms.
A variety of Multimedia software is available from MpegTV, some of it for Linux/Alpha.
Also be sure to read through the AlphaLinux.Org Software pages for more commercial and non-commercial software.
Aside from the above native applications many Linux/x86 applications can be run under Linux/Alpha using the em86 emulator. See Section em86 for details.