You can manually repair the registry with Microsoft’s regedit.exe invoked from the command line. There are many utilities to automatically find and fix problems. They usually have free trials that will detect but not fix anything. Before trying any of this sort of software, do a full backup. If it fails, you may have to reinstall Windows and all your applications from scratch.

Registry Fixup Utilities
Product	Price in mindprod.com CurrCon international currency Applet needs Java installed for it to display prices in any world currency. mindprod.com CurrCon international currency Applet needs Java installed for it to display prices in any world currency.	Notes
Registry Repair Pro	$10.00 USD	Download Trial. The trial will make only 15 corrections. The program does nothing but delete registry entries and dead links. They accept PayPal. It found 481 problems vs Ace’s 176. I did not buy the program, so I don’t know how many of those could safely be deleted.W98/Me/NT/W2K/XP/W2K3/Vista
RegClean	$20.00 USD	Download Trial. Nothing to configure. Does not let you configure what to scan or what to leave intact. Works under Vista. Has a quite confusing registration process. It seems to want you to provide a serial number before you purchase.
Registry First Aid	$28.00 USD for the standard edition and $48.00 USD for the platinum edition	Download Trial. The claim to fame of this program is it not only deleted damaged registry entries, it tries to fix them by finding moved files. Works under W2K/XP/W2K3/Vista. The pro version includes an autorun manager. Last revised 2007-05-20..
Ace Utilities	$30.00 USD	Download Trial. Works under W2K/XP/W2K3/Vista. This is what I was using personally. Found a whopping 713 problems in my test. It found another 123 when I turned on the thorough mode option. Designed for the experienced programmer. Registry repair, basically finds broken links and lets you either manually repair them or delete them. It will invoke the regedit for you on any problem it finds to let you hack a fix. Has a feature to clean out broken uninstalls. It includes an autorun manager, find duplicate files, remove junk files, delete (but not fix) broken shortcuts, secure delete, find empty folders, disk space analysis, empty directory finder. Not for the novice. For example, you could badly screw up the universe if you willy nilly deleted empty folders. I bought it and gradually came to trust it, and now I have it set up to automatically once a day clean my registry in thorough mode without confirmation o on Win2K. It has not screwed anything up yet. I am used it successfully without incident under W2K. However, under XP I suspect it may have been too eager. It destroyed an registry entries that stoped Acer NTI backup and DVD/CD maker from working. It also blew Visual C++ Studio out the water. Acer restore undid that mistake and NTI started working again. However, under Vista, Ace destroyed a crucial registry entry that made the machine unbootable. It took weeks to get it working again. Last revised 2007-08-26.
RegistryBooster 2	$30.00 USD	Download Trial. Works under W2K/XP/Vista. Does not work under Vista-64 bit. Found 90% of the problems Ace found. It is unusually quick. It can also defrag the registry, but does not compact or optimise its order the way NTRegOpt does. Its big plus is it is Microsoft certified and marketed by the Winzip people. This is reassurance it won’t do serious damage. It improperly deletes Java preferences entries. It is confused by Java’s goofy /-notation to mark capital letters. This is what I am using personally now. The graphics and the website are beautifully done. Last revised 2007-10-28.
RegCure Registry Fixup	$30.00 USD	Download Trial. review. Found 700 errors in a newly installed Vista system, mostly empty registry keys and fragments left behind by programs that did not fully uninstall themselves. It also has an autorun manager. Very easy to use. Trial version detects all classes of error, but fixes only two. It claims to clean up DLLs and broken Java installs. Works under W2K/XP/W2K3/Vista. Last revised 2007-04-18..
Registry Mechanic	$30.00 USD	Download Trial. Created by PCTools. Trial version detects all classes of error, but fixes only some. It removes removed entries for uninstalls for non-existent logs. I think this was not wise. The logs may be created in future, but before uninstall. It was sightly confusing to use. The registered version can compact registries. It does a system optimisation but tells you nothing about what it changed. It does offer to roll back the changes however. The display overflowed its box so it was not possible to read it all. Works under W2K/XP/W2K3/Vista. Last revised 2007-04-20.
Registry Fix	$37.00 USD	Download Trial review. Found 404 problems in my test. Granted, many of them are not serious, like dangling recently looked at file lists in various programs that you have since deleted. Specialises in just registry repair. It has a primitive autorun manager to stop programs from autostarting at boot time. The trial version refuses to fix anything so you can’t really test it for safety. What you can do is manually fix some of the problems it finds, simulating what it would do to see if anything explodes. My own such experiments have been safe so far. Since it is so expensive I am loathe to fork out the dough without assuring myself it will work. It still did not detect the cause of an empty entry in my Add-Remove programs table.
Vilma Software Oberon	$39.00 USD	Download Trial. This is a different sort of product from the usual registry fixer. It is a programmer’s tool to rapidly search and modify the registry. It also finds and corrects invalid entries. it will optimise the registry by defragmenting and reducing it’s size. It will find and replace data in all registry entries (and keys) including binary types. With the Registry Explorer you don’t have to explicitly back up the registry, when you experiment on it, because the Registry Explorer does that in the background. If you decide to undo some change to you made, just open the Backup window and restore the item with a click. The Registry Inspector checks the registry for invalid entries, bad file system references, orphaned installed files, invalid application paths. It checks the fonts, startup section, program integrity, shortcuts and the errors in the COM (Component Object Model) sections. Startup Manager is an autorun manager to control which applications run at startup.
Tuneup Utilities	$40.00 USD	Download Trial. This is a very comprehensive set of utilities with a beautifully done user interface and polished graphics. This is aimed at the naive user who wants a simple automatic program that does not ask a lot of technical questions. Among other things it does the following: The registry cleaner found 297 problems, mostly old history. Unlike other registry cleaners it tells you in fairly clear English why each entry it has found is invalid. You cannot configure it to permanently avoid removing dangerous entries. It has a registry defragger that does not require reboot. utilities to simplify and enhance the Control Panel functions. Disk cleaner, very simple, not configurable. Disk space analyser. It optimises TCP/IP connections including tweaking some obscure settings in IE and Firefox. It has a file or folder shredder for secure delete. It does not however wipe free space of already deleted files. It was made in Germany.
SysTweak Advanced System Optimiser	$40.00 USD	Download Trial. Found 130 problems in my test. Does registry repair plus a lot more. Designed for the novice. Clean out the registry of deadwood. This shrinks the registry, making it faster. It also gets rid of most of the deadwood in the list of programs that won’t uninstall but whose files have been manually removed. Defrag the registry, similar to defragging a disk to put it in order for fast access and collect the scattered bits of it together. Get rid of junk files, much like Norton Clean Sweep, but easier to understand and configure, and with several options so you can back out selectively if you remove too much. An autorun manager utility like Startup Cop to stop programs from autostarting at boot time. It has a database to tell you what all the programs are and whether they can be safely deleted. System information, like Norton SI. Optimising advisor. Secure delete, like Norton Wipe. Find duplicate files (quite slow). Repair damaged Zip files. It is a remarkably safe tool in the hands of a novice. The only thing they could get in trouble with is using an unconfigured file deleter, which could wipe out valuable files. The trial version actually fixes problems, so you can truly test the program for compatibility and safety. More detail.
PC Onpoint	secret, presumably only revealed during the registration process.	Download Trial. review. Other than the usual registry problems it finds: Missing file associations Missing startup programs Invalid device drivers Invalid application paths Missing DLL files Missing help files Missing system fonts Invalid Shortcuts The downloadable free scan is a bit of a joke since it does not fix the problems or give you any details. All it does it claim to have found x errors. That demonstrates nothing.
RegSweep Registry Fixup	secret, presumably only revealed during the registration process.	Download Trial. review. Not tried.
RegistrySmart	secret, presumably only revealed during the registration process.	Download Trial. review. Not tried. Works under Vista.
Error Doctor	secret, presumably only revealed during the registration process.	Download Trial. review. Not tried.

Downside

These programs don’t actually repair the registry. All they do is mindlessly delete damaged or useless entries and leave it up to the programs that use them to rebuild them or you to manually rebuild them for example by reinstalling software, or by setting up your extension associations again. However, the good news is this brute force approach seems to cause very little in the way of problems. The benefit is mainly psychological getting rid of the trash. It does not make a big difference to performance.

None of these utilities were able to fix my broken Java installation registry entries that were stopping me from either reinstalling Java or uninstalling it. I would have to write my own specialised tool for that. None of them offered me a search function through the problems to look for the ones likely causing the problem I want to fix.

I suspect many of these registry fixers are actually almost the same product marketed under different names to give the illusion of competition. I would take any reviews with a large grain of salt. I don’t have much faith in a company that refuses to tell you up front how much their product costs, or who try to trick you into thinking it is free.