The 1541/1571 Alignment system is probably the most well known alignment software. Not only will this software tell you if you drive is aligned, it also gives instructions on how to fix your alignment. This program requires a calibrated disk.

This handy alignment utility is a little different than the others I've seen because it lets you manually move the head between track 1 & 35 while checking alignment results.

1541 Allignment (programmers spelling, not mine) by ANTIRAM in 1984.  If you don't know what this is for you probably don't want it.

Written by Greg Granville - 1541 Alignment Check is one of the few (if not only) drive checker that is run with a joystick. Kinda curious why someone would create a utility like this with joystick control.

1541 Alps Drive Check goes beyond the usual alignment check and speed test, it also checks the drive LED, stepper motor, Stop limits, disk read/write and write protect. Also works on devices other just 8.

Besides the usual head alignment test, this program will also test disk rotation speed.

Originally programmed by E. Clutter and printed in Transactor magazine on January 1986 (page 13), this version has been extensively modified by Darrell G. Shannon and Lowell Wm to add support for the 1581 drive.

This version of Align Check is a further modification of Align Check v2. Bob McCullough added support for testing both sides of the 1571 disk drive and some menu changes on April 4th, 1990.

Alps Aligner is a program that will aid in aligning a 1541 drive head.  Alps was a popular brand of drive mechanism in the 1541 hence the name.

Although this program likely needs a special alignment floppy to do an actual alignment of your 1541 floppy drive, the other feature that could be useful is the option to spin the drive so you can use a head cleaning disk.

With the 1541 DISK DRIVE ALIGNMENT PROGRAM you can align the drive yourself In an hour or so. Not only that. you can do It at home AND no special equipment Is required. Anyone with average mechanical skills can do It!

Written by Disk Surgeon, Disk Exerciser will position your head and stopper to the optimum position allowable to your disk drive. There are some basic instructions in the program. I believe these type of programs require a specially formatted floppy.

Diskaligner is a program for aligning the head of a 1541 floppy drive on the Commodore 64.  This program does not work at all in emulation.  I have tried under VICE, Z64K, CCS64 and DENISE and they all lock up when checking for drive presence. I have however tested it successfully on a stock 64C and it works fine.  For screenshots and some additional information, check out this link at the C64 Copy Protection website.

Here is a link to the manual.

Update - A generous visitor to the website (Thx Mila) kindly shared a version of Diskagliner that has been cracked/fixed to work also in emulators.  I have added this new version to the archive but also left the original that only works on real hardware.